From c3a0ee4001a330cabe659ea8eb7255be23f4ae05 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Fri, 29 Jul 2022 18:17:46 -0700
Subject: [PATCH 01/29] Adding Cython StepVector to the project

---
 tiny/rna/counter/stepvector/__init__.py       |   1 +
 tiny/rna/counter/stepvector/__init__.pyx      |   0
 tiny/rna/counter/stepvector/_stepvector.pxd   |  45 ++++
 tiny/rna/counter/stepvector/_stepvector.pyx   | 177 ++++++++++++++
 tiny/rna/counter/stepvector/src/PyRef.h       |  89 +++++++
 .../rna/counter/stepvector/src/StepVector.cpp | 219 ++++++++++++++++++
 tiny/rna/counter/stepvector/src/StepVector.h  |  32 +++
 7 files changed, 563 insertions(+)
 create mode 100644 tiny/rna/counter/stepvector/__init__.py
 create mode 100644 tiny/rna/counter/stepvector/__init__.pyx
 create mode 100644 tiny/rna/counter/stepvector/_stepvector.pxd
 create mode 100644 tiny/rna/counter/stepvector/_stepvector.pyx
 create mode 100644 tiny/rna/counter/stepvector/src/PyRef.h
 create mode 100644 tiny/rna/counter/stepvector/src/StepVector.cpp
 create mode 100644 tiny/rna/counter/stepvector/src/StepVector.h

diff --git a/tiny/rna/counter/stepvector/__init__.py b/tiny/rna/counter/stepvector/__init__.py
new file mode 100644
index 00000000..97932c73
--- /dev/null
+++ b/tiny/rna/counter/stepvector/__init__.py
@@ -0,0 +1 @@
+from ._stepvector import StepVector
\ No newline at end of file
diff --git a/tiny/rna/counter/stepvector/__init__.pyx b/tiny/rna/counter/stepvector/__init__.pyx
new file mode 100644
index 00000000..e69de29b
diff --git a/tiny/rna/counter/stepvector/_stepvector.pxd b/tiny/rna/counter/stepvector/_stepvector.pxd
new file mode 100644
index 00000000..df485bd9
--- /dev/null
+++ b/tiny/rna/counter/stepvector/_stepvector.pxd
@@ -0,0 +1,45 @@
+# distutils: language = c++
+# cython: language_level = 3
+
+from cpython.ref cimport PyObject
+from libcpp.map cimport map as ccmap
+
+ctypedef PyObject* PyPtr
+
+cdef extern from "src/PyRef.h" namespace "PyPtr":
+    cdef cppclass PyRef:
+        PyRef() except +
+        PyRef(PyObject* set_obj) except +
+        PyObject* get() const
+        PyRef& operator+(const PyRef &po)
+
+cdef extern from "src/StepVector.cpp":
+    pass
+
+cdef extern from "src/StepVector.h" namespace "sparse_vectors":
+    cdef cppclass _StepVector[T]:
+        ctypedef ccmap[long int, T].const_iterator const_iterator
+
+        _StepVector() except +
+
+        long int min_index
+        long int max_index
+
+        T operator[](long int i) const
+        void set_value(long int start, long int end, T value) except +
+        void add_value(long int start, long int end, T value) except +
+        void apply_to_values(long int start, long int end, void (*func)(T &val))
+        long int num_values() const
+        const_iterator get_values(long int start) const
+        const_iterator begin() const
+        const_iterator end() const
+
+cdef class StepVector:
+    cdef _StepVector[PyRef] *c_step
+    cdef long int start
+    cdef long int stop
+    cdef char _typecode
+    @staticmethod
+    cdef void _construct_wrapper(StepVector obj)
+    @staticmethod
+    cdef void _set_wrapper(StepVector obj, _StepVector[PyRef] *ref)
diff --git a/tiny/rna/counter/stepvector/_stepvector.pyx b/tiny/rna/counter/stepvector/_stepvector.pyx
new file mode 100644
index 00000000..47f30f8a
--- /dev/null
+++ b/tiny/rna/counter/stepvector/_stepvector.pyx
@@ -0,0 +1,177 @@
+# distutils: language = c++
+# cython: language_level = 3
+
+import sys
+import HTSeq
+
+from cython.operator cimport dereference as deref, postincrement as cni
+
+cdef class StepVector:
+
+    @classmethod
+    def create(cls, *args, **kwargs):
+        cdef StepVector self = StepVector(*args, **kwargs)
+        StepVector._construct_wrapper(self)
+        return self
+
+    def __cinit__(self, length = sys.maxsize, typecode = 'O', start_index = 0):
+        self.c_step = NULL
+        self._typecode = ord(typecode)
+        self.start = start_index
+        self.stop = start_index + length
+
+    @staticmethod
+    cdef void _construct_wrapper(StepVector obj):
+        obj.c_step = new _StepVector[PyRef]()
+
+    @staticmethod
+    cdef void _set_wrapper(StepVector obj, _StepVector[PyRef] *ref):
+        obj.c_step = ref
+
+    def __setitem__(self, index, value):
+        if isinstance(value, StepVector):
+            if value.start == index.start and value.stop == index.stop:
+                return
+            else:
+                raise NotImplemented("Stepvector-to-Stepvector assignment still missing")
+        if isinstance(index, slice):
+            if index.step is not None and index.step != 1:
+                raise ValueError("Striding slices (i.e., step != 1) are not supported")
+            if index.start is None:
+                start = self.start
+            else:
+                if index.start < self.start:
+                    raise IndexError("start too small")
+                start = index.start
+            if index.stop is None:
+                stop = self.stop
+            else:
+                if index.stop > self.stop:
+                    raise IndexError("stop too large")
+                stop = index.stop
+            # Note the "-1": The C++ object uses closed intervals, but we follow
+            # Python convention here and use half-open ones.
+            self.c_step.set_value(start, stop-1, PyRef(<PyPtr>value))
+        else:
+            self.c_step.set_value(index, index, PyRef(<PyPtr>value))
+
+    def get_steps(self, values_only = False, merge_steps = True):
+        cdef _StepVector[PyRef].const_iterator startvals
+        cdef set value, prevval
+        startvals = self.c_step.get_values(self.start)
+        prevstart = self.start
+
+        # Iterator bounds check until a better solution is written
+        if startvals == self.c_step.end():
+            yield (self.start, self.stop, set())
+            return
+        else:
+            prevval = <set>deref(cni(startvals)).second.get()
+
+        while startvals != self.c_step.end():
+            pair = deref(cni(startvals))
+            stepstart, value = <long int>pair.first, <set>pair.second.get()
+            if merge_steps and value == prevval:
+                continue
+            if self.stop is not None and stepstart >= self.stop:
+                if not values_only:
+                    yield prevstart, self.stop, prevval
+                else:
+                    yield prevval
+                return
+            if not values_only:
+                yield prevstart, stepstart, prevval
+            else:
+                yield prevval
+            prevstart, prevval = stepstart, value
+        else:
+            if not values_only:
+                yield prevstart, min(self.stop, self.c_step.max_index), prevval
+            else:
+                yield prevval
+
+    def __getitem__(self, index):
+        cdef StepVector res
+        cdef int start
+        cdef int stop
+
+        if isinstance(index, slice):
+            if index.step is not None and index.step != 1:
+                raise ValueError("Striding slices (i.e., step != 1) are not supported")
+            if index.start is None:
+                start = self.start
+            else:
+                if index.start < self.start:
+                    raise IndexError("start too small")
+                start = index.start
+            if index.stop is None:
+                stop = self.stop
+            else:
+                if index.stop > self.stop:
+                    raise IndexError("stop too large")
+                stop = index.stop
+            res = StepVector(stop - start, 'O', start)
+            StepVector._set_wrapper(res, self.c_step)
+            res.start = start
+            res.stop = stop
+            return res
+        else:
+            return <set>deref(self.c_step.get_values(index)).second.get()
+
+    def __iter__(self):
+        for start, stop, value in self.get_steps():
+            for i in range(start, stop):
+                yield value
+
+    def __repr__(self):
+        if self.start == -sys.maxsize - 1:
+            start_s = "-inf"
+        else:
+            start_s = str(self.start)
+        if self.stop == sys.maxsize:
+            stop_s = "inf"
+        else:
+            stop_s = str(self.stop)
+        return "<%s object, type '%s', index range %s:%s, %d step(s)>" % (
+            self.__class__.__name__, self.typecode(), start_s,
+            stop_s, self.num_steps())
+
+    def typecode(self):
+        return chr(self._typecode)
+
+    @property
+    def start(self):
+        return self.start
+
+    @property
+    def stop(self):
+        return self.stop
+
+    @start.setter
+    def start(self, value):
+        self.start = value
+
+    @stop.setter
+    def stop(self, value):
+        self.stop = value
+
+    def __len__(self):
+        return self.stop - self.start
+
+    def num_steps(self):
+        return self.c_step.num_values()
+
+    def __iadd__(self, value):
+        cdef PyRef ref = PyRef(<PyPtr>value)
+        self.c_step.add_value(self.start, self.stop-1, ref)
+        return self
+
+    # Todo
+    def __eq__(self, other): pass
+    def __reduce__(self): pass
+    def apply(self, func, start=None, stop=None): pass
+
+    @property
+    def __class__(self):
+        """~~master_of_disguise.exe~~"""
+        return HTSeq.StepVector.StepVector
\ No newline at end of file
diff --git a/tiny/rna/counter/stepvector/src/PyRef.h b/tiny/rna/counter/stepvector/src/PyRef.h
new file mode 100644
index 00000000..37014b28
--- /dev/null
+++ b/tiny/rna/counter/stepvector/src/PyRef.h
@@ -0,0 +1,89 @@
+#include "Python.h"
+#include <iostream>
+
+namespace PyPtr {
+    class PyRef {
+        PyObject* obj;
+
+        public:
+            PyObject* get() const {return obj;}
+
+            // Default constructor
+            PyRef() {
+                obj = NULL;
+            }
+
+            // Obj constructor
+            PyRef(PyObject* obj) {
+                if (PySet_Check(obj)){
+                    this->obj = obj;
+                } else {
+                    // PySet_New treats the argument as an iterable
+                    // We don't want that, e.g. if adding a tuple
+                    // PySet_Add simply adds without iteration
+                    this->obj = PySet_New(NULL);
+                    PySet_Add(this->obj, obj);
+                }
+                Py_XINCREF(this->obj);
+            }
+
+            // Destructor
+            ~PyRef() {
+                Py_XDECREF(obj);
+            }
+
+            // Copy constructor
+            PyRef(const PyRef& other) {
+                obj = PySet_New(other.obj);
+                Py_XINCREF(obj);
+                Py_XDECREF(other.obj);
+            }
+
+            // Move constructor
+            PyRef(PyRef&& other) {
+                obj = other.obj;
+                Py_XDECREF(other.obj);
+            }
+
+            // Assignment
+            PyRef& operator=(const PyRef& other) {
+                Py_XDECREF(obj);
+                obj = other.obj;
+                Py_XINCREF(obj);
+                return *this;
+            }
+
+            // Move assignment
+            PyRef& operator=(PyRef&& other) {
+                Py_XDECREF(obj);
+                obj = PySet_New(other.obj);
+                Py_XINCREF(obj);
+                other.obj = NULL;
+                return *this;
+            }
+
+            PyRef& operator+= (const PyRef& other) {
+                if (PySet_Check(other.obj)){
+                    _PySet_Update(this->obj, PyObject_GetIter(other.obj));
+                } else {
+                    PySet_Add(this->obj, other.obj);
+                }
+                return *this;
+            }
+
+            PyRef operator+ (const PyRef& other) {
+                PyRef result(obj);
+                if (PySet_Check(other.obj)){
+                    _PySet_Update(result.obj, PyObject_GetIter(other.obj));
+                } else {
+                    PySet_Add(result.obj, other.obj);
+                }
+                Py_XINCREF(result.obj);
+                return result;
+            }
+
+            bool operator== (const PyRef &other) const {
+                return PyObject_RichCompareBool(obj, other.obj, Py_EQ);
+            }
+    };
+}
\ No newline at end of file
diff --git a/tiny/rna/counter/stepvector/src/StepVector.cpp b/tiny/rna/counter/stepvector/src/StepVector.cpp
new file mode 100644
index 00000000..f07ca296
--- /dev/null
+++ b/tiny/rna/counter/stepvector/src/StepVector.cpp
@@ -0,0 +1,219 @@
+#include "StepVector.h"
+
+using namespace sparse_vectors;
+
+template <class T> _StepVector<T>::_StepVector() { m[min_index] = T(); }
+
+template <class T> const long int _StepVector<T>::min_index = LONG_MIN;
+
+template <class T> const long int _StepVector<T>::max_index = LONG_MAX;
+
+template <class T> const T _StepVector<T>::operator[](long int i) const {
+    const_iterator it = m.upper_bound(i);
+    it--;
+    return it->second;
+}
+
+template <class T>
+void _StepVector<T>::set_value(long int from, long int to, T value) {
+    if (from > to)
+        throw std::out_of_range("Indices reversed in StepVector.");
+
+    // Unless the new step extends to the end, we need to insert a new
+    // value afterwards unless the step to the right has the same value
+    if (to < max_index) {
+        T next_value = (*this)[to + 1];
+        if (!(next_value == value))
+            m[to + 1] = next_value;
+    }
+
+    // Find the left step, i.e., the step whose start is smaller or equal
+    // to 'from':
+    typename std::map<long int, T>::iterator left = m.upper_bound(from);
+    left--;
+    assert(left->first <= from);
+
+    // Get rid of the steps present between from and to
+    typename std::map<long int, T>::iterator it = m.lower_bound(from);
+    if (it->first == from)
+        it++;
+    assert(it->first > from);
+    if (it->first <= to) {
+        m.erase(it, m.upper_bound(to));
+    }
+
+    if (!(left->second == value)) {
+        if (left->first != from)
+            // Insert a new step
+            m[from] = value;
+        else {
+            // We have from == left->first, so the step is already present.
+            // Would changing m[from] to value make it equal to its left
+            // neighbor?
+            if (left == m.begin())
+                // no, there is no left neighbor
+                m[from] = value;
+            else {
+                typename std::map<long int, T>::iterator leftleft = left;
+                leftleft--;
+                if (!(leftleft->second == value))
+                    // ok, change the value
+                    m[from] = value;
+                else
+                    // no, rather delete the step
+                    m.erase(left);
+            }
+        }
+    }
+}
+
+bool debug = false;
+template <class T>
+void _StepVector<T>::add_value(long int from, long int to, T value) {
+    if (debug) {
+        std::cout << std::endl << "Begin: " << std::flush;
+        PyObject_Print(value.get(), stdout, 0);
+        std::cout << std::endl << std::flush;
+    }
+    if (from > to)
+        throw std::out_of_range("Indices reversed in StepVector.");
+
+    if (to < max_index) {
+        T next_value = (*this)[to + 1];
+        auto before = m[to + 1];
+        m[to + 1] = next_value;
+        if (debug) {
+            std::cout << to + 1 << ": setting \"next\" from: ";
+            PyObject_Print(before.get(), stdout, 0);
+            std::cout << " to ";
+            PyObject_Print(m[to + 1].get(), stdout, 0);
+            std::cout << " (" << m[to+1].get() << ") " << std::endl;
+        }
+    }
+
+    typename std::map<long int, T>::iterator it = m.upper_bound(from);
+    it--;
+    bool need_to_insert_step_at_from = it->first < from;
+    T old_val_at_from;
+    if (need_to_insert_step_at_from) {
+        old_val_at_from = it->second;
+        it++;
+    }
+    // Now, it points to the first element with it->first >= from
+
+    for (; it != m.end() && it->first <= to; it++){
+        if (debug){
+            std::cout << it->first << ": adding to ";
+            PyObject_Print(it->second.get(), stdout, Py_PRINT_RAW);
+            std::cout << " (" << it->second.get() << ") " << std::endl;
+        }
+
+        it->second += value;
+    }
+
+    if (need_to_insert_step_at_from){
+        m[from] = old_val_at_from + value;
+        if (debug){
+            std::cout << from << ": inserting step into ";
+            PyObject_Print(old_val_at_from.get(), stdout, Py_PRINT_RAW);
+            std::cout << " (" << old_val_at_from.get() << ") " << std::endl;
+        }
+    }
+}
+
+template <class T>
+void _StepVector<T>::apply_to_values(long int from, long int to, void (*func)(T &val)) {
+    if (from > to)
+        throw std::out_of_range("Indices reversed in StepVector.");
+
+    if (to < max_index) {
+        T next_value = (*this)[to + 1];
+        m[to + 1] = next_value;
+    }
+
+    typename std::map<long int, T>::iterator it = m.upper_bound(from);
+    it--;
+    bool need_to_insert_step_at_from = it->first < from;
+    T old_val_at_from;
+    if (need_to_insert_step_at_from) {
+        old_val_at_from = it->second;
+        it++;
+    }
+    // Now, it points to the first element with it->first >= from
+
+    for (; it != m.end() && it->first <= to; it++)
+        func(it->second);
+
+    if (need_to_insert_step_at_from) {
+        func(old_val_at_from);
+        m[from] = old_val_at_from;
+    }
+}
+
+template <class T>
+typename _StepVector<T>::const_iterator
+_StepVector<T>::get_values(long int from) const {
+    return --m.upper_bound(from);
+}
+
+template< class T >
+long int _StepVector<T>::num_values( ) const{
+  return this->m.size();
+}
+
+template <class T>
+typename _StepVector<T>::const_iterator
+_StepVector<T>::begin() const {
+    return m.begin();
+}
+
+template <class T>
+typename _StepVector<T>::const_iterator
+_StepVector<T>::end() const {
+    return m.end();
+}
+
+//template<class T>
+//iterator::iterator(){
+//    current = m.begin()
+//    last = m.end()
+//}
+//
+//template<class T>
+//iterator::iterator(typename const_iterator from){
+//    current = from
+//    last = m.end()
+//}
+//
+//template<class T>
+//std::pair<long int, T>& iterator::operator*(){return current;}
+//
+//template<class T>
+//iterator iterator::operator++(){
+//    if (current == last){
+//        PyErr_SetString(PyExc_StopIteration, "Reached StepVector end");
+//        return NULL;
+//    } else {
+//        return *current++;
+//    }
+//}
+//
+//template<class T>
+//iterator iterator::operator--(){
+//    if (current == begin()){
+//        PyErr_SetString(PyExc_StopIteration, "Reached StepVector start");}
+//        return NULL;
+//    } else {
+//        return *current--;
+//    }
+//}
+//
+//template<class T>
+//bool iterator::operator==(const iterator other){
+//    return current == other.current;
+//}
+//
+//template<class T>
+//bool iterator::operator!=(const iterator other){
+//    return current != other.current;
+//}
\ No newline at end of file
diff --git a/tiny/rna/counter/stepvector/src/StepVector.h b/tiny/rna/counter/stepvector/src/StepVector.h
new file mode 100644
index 00000000..ee64a316
--- /dev/null
+++ b/tiny/rna/counter/stepvector/src/StepVector.h
@@ -0,0 +1,32 @@
+#ifndef _STEP_VECTOR_H_
+#define _STEP_VECTOR_H_
+
+#include <map>
+#include <stdexcept>
+#include <climits>
+#include <iostream>  //for now only
+
+#include "Python.h"
+
+namespace sparse_vectors {
+    template< class T >
+    class _StepVector {
+        protected:
+            std::map< long int, T > m;
+        public:
+            typedef typename std::map< long int, T >::const_iterator const_iterator;
+            static const long int min_index;
+            static const long int max_index;
+            _StepVector( );
+            const T operator[]( long int i ) const;
+            void set_value( long int from, long int to, T value );
+            void add_value( long int from, long int to, T value );
+            void apply_to_values( long int from, long int to, void (*func)( T & val ) );
+            long int num_values( ) const;
+            const_iterator get_values( long int from ) const;
+            const_iterator begin( ) const;
+            const_iterator end( ) const;
+    };
+};
+
+#endif //_STEP_VECTOR_H_
\ No newline at end of file

From 4619b6a02d2c0f7009bb557d70d33e4a48d1829c Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Fri, 29 Jul 2022 18:19:54 -0700
Subject: [PATCH 02/29] Adding Cythonization to setup.py. This is currently a
 macOS-only implementation. Linux compatability requires essentially removing
 the extra_*_args kwds, but further testing is needed on both Linux and macOS

---
 setup.py | 33 ++++++++++++++++++++++++---------
 1 file changed, 24 insertions(+), 9 deletions(-)

diff --git a/setup.py b/setup.py
index d0bd6109..cc79fd94 100644
--- a/setup.py
+++ b/setup.py
@@ -4,6 +4,7 @@
 import setuptools
 
 from setuptools.command.install import install
+from Cython.Build import cythonize
 
 # Package metadata
 NAME = 'tinyrna'
@@ -14,20 +15,29 @@
 PLATFORM = 'Unix'
 REQUIRES_PYTHON = '>=3.7.0'
 VERSION = '0.1'
+REQUIRED = []  # Required packages are installed via Conda's environment.yml
 
-# Required packages are installed via Conda's environment.yml
-# See PreFlight below...
-REQUIRED = []
 
-
-class PreFlight(install):
+class PrereqAndExec(install):
     def run(self):
-        if not all([os.getenv(conda_var) for conda_var in ["CONDA_PREFIX", "CONDA_DEFAULT_ENV"]]):
-            sys.exit("CRITICAL ERROR: you appear to be installing %s outside of a conda environment.\n"
-                     "Instead, please run: ./setup.sh" % (NAME,))
+        if not self.in_conda_env():
+            sys.exit("CRITICAL ERROR: you appear to be installing %s outside of a conda environment.\n" % (NAME,) +
+                     "Instead, please run: ./setup.sh" )
         else:
             install.run(self)
 
+    def in_conda_env(self):
+        return all([os.getenv(conda_var) for conda_var in ["CONDA_PREFIX", "CONDA_DEFAULT_ENV"]])
+
+debug_cython = False
+cython_extensions = [
+    setuptools.Extension(
+        "tiny.rna.counter.stepvector._stepvector",
+        sources=['tiny/rna/counter/stepvector/_stepvector.pyx'],
+        extra_compile_args=['-isystem', '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include', '-stdlib=libc++', '-std=c++11'],
+        extra_link_args=['-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib'],
+        language='c++')
+]
 
 setuptools.setup(
     name=NAME,
@@ -35,7 +45,7 @@ def run(self):
     author=AUTHOR,
     author_email=EMAIL,
     description=DESCRIPTION,
-    cmdclass={'install': PreFlight},
+    cmdclass={'install': PrereqAndExec},
     include_package_data=True,
     packages=['tiny'],
     zip_safe=False,
@@ -48,6 +58,11 @@ def run(self):
             'tiny-plot = tiny.rna.plotter:main'
         ]
     },
+    ext_modules=cythonize(
+        cython_extensions,
+        compiler_directives={'language_level': '3'},
+        gdb_debug=debug_cython
+    ),
     scripts=['tiny/rna/tiny-deseq.r'],
     classifiers=[
         'Programming Language :: Python :: 3',

From ee577a460b767c3e600126b1b4bb17e413e8ad0d Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Fri, 29 Jul 2022 18:27:04 -0700
Subject: [PATCH 03/29] Integrating the Cython StepVector with ReferenceTables.
 The necessary changes are actually pretty minimal. There's some extra fluff
 here to make switching between Cython and HTSeq StepVector easier

---
 tiny/rna/counter/hts_parsing.py | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/tiny/rna/counter/hts_parsing.py b/tiny/rna/counter/hts_parsing.py
index 43925a11..178c4e4c 100644
--- a/tiny/rna/counter/hts_parsing.py
+++ b/tiny/rna/counter/hts_parsing.py
@@ -351,7 +351,11 @@ def __init__(self, gff_files: Dict[str, list], feature_selector, **kwargs):
         self._set_filters(**kwargs)
         self.gff_files = gff_files
         # ----------------------------------------------------------- Primary Key:
-        self.feats = HTSeq.GenomicArrayOfSets("auto", stranded=False)   # Root Match ID
+        if use_cython_stepvector:
+            self.feats = HTSeq.GenomicArray("auto", stranded=False)         # Root Match ID
+        else:
+            self.feats = HTSeq.GenomicArrayOfSets("auto", stranded=False)   # Root Match ID
+
         self.parents, self.filtered = {}, set()                         # Original Feature ID
         self.intervals = defaultdict(list)                              # Root Feature ID
         self.matches = defaultdict(set)                                 # Root Match ID
@@ -362,6 +366,10 @@ def __init__(self, gff_files: Dict[str, list], feature_selector, **kwargs):
         # Patch the GFF attribute parser to support comma separated attribute value lists
         setattr(HTSeq.features.GFF_Reader, 'parse_GFF_attribute_string', staticmethod(parse_GFF_attribute_string))
 
+        # Patch HTSeq's StepVector with our Cython implementation (60% faster)
+        if use_cython_stepvector:
+            setattr(HTSeq.StepVector, 'StepVector', StepVector)
+
     @report_execution_time("GFF parsing")
     def get(self) -> Tuple[StepVector, AliasTable, ClassTable, dict]:
         """Initiates GFF parsing and returns the resulting reference tables"""

From 831069fda7a3a447a79f86193556db26d99213bf Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sat, 30 Jul 2022 11:25:58 -0700
Subject: [PATCH 04/29] Got my branches a little tangled. These changes were
 intended for the last commit, but it has already been pushed to origin.

---
 tiny/rna/counter/hts_parsing.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tiny/rna/counter/hts_parsing.py b/tiny/rna/counter/hts_parsing.py
index 178c4e4c..5e991385 100644
--- a/tiny/rna/counter/hts_parsing.py
+++ b/tiny/rna/counter/hts_parsing.py
@@ -317,6 +317,10 @@ def not_implemented(self):
 StepVector = HTSeq.GenomicArrayOfSets
 Tags = DefaultDict[str, Set[str]]
 
+use_cython_stepvector = True
+if use_cython_stepvector:
+    from tiny.rna.counter.stepvector import StepVector
+    setattr(HTSeq.StepVector, 'StepVector', StepVector)
 
 class ReferenceTables:
     """A GFF parser which builds feature, alias, and class reference tables
@@ -366,10 +370,6 @@ def __init__(self, gff_files: Dict[str, list], feature_selector, **kwargs):
         # Patch the GFF attribute parser to support comma separated attribute value lists
         setattr(HTSeq.features.GFF_Reader, 'parse_GFF_attribute_string', staticmethod(parse_GFF_attribute_string))
 
-        # Patch HTSeq's StepVector with our Cython implementation (60% faster)
-        if use_cython_stepvector:
-            setattr(HTSeq.StepVector, 'StepVector', StepVector)
-
     @report_execution_time("GFF parsing")
     def get(self) -> Tuple[StepVector, AliasTable, ClassTable, dict]:
         """Initiates GFF parsing and returns the resulting reference tables"""

From 95dec150c0e580cf25f08399b7d3b196b25ac647 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sun, 14 Aug 2022 11:15:48 -0700
Subject: [PATCH 05/29] Native Python efficiency improvements:

After doing a lot of profiling and fiddling with the routine in FeatureSelector.choose(), I'm once again back to flattening the list of Stage 2 candidates via a list comprehension. 1/2 of Stage 2 is performed in the comp., and step 2/2 (calculating min_rank) is now performed with one call on the resulting list. While runtimes are better with this approach, elimination by hierarchy is still flawed.

I've also removed the inner generator expression in FeatureCounter.assign_features(). After the recent switch to calling union(*) on StepVector steps, it really doesn't make sense to screen for zero length step sets. This is much more efficient.

Strands are now represented with a boolean value which simplifies some things. Strand selection is now performed via a chain of bitwise XOR operations. This prevents us from having to form and pass a tuple for each evaluation.
---
 tiny/rna/counter/features.py    | 58 +++++++++++++++++++--------------
 tiny/rna/counter/hts_parsing.py | 12 +++----
 tiny/rna/counter/matching.py    |  2 +-
 tiny/rna/counter/statistics.py  |  8 ++---
 4 files changed, 45 insertions(+), 35 deletions(-)

diff --git a/tiny/rna/counter/features.py b/tiny/rna/counter/features.py
index 785b6567..ee43f0d5 100644
--- a/tiny/rna/counter/features.py
+++ b/tiny/rna/counter/features.py
@@ -43,12 +43,10 @@ def assign_features(self, al: dict) -> Tuple[dict, int]:
         feat_matches, assignment = set(), {}
 
         try:
-            feat_matches = feat_matches.union(*(match for match in
-                    (Features.chrom_vectors[al['chrom']]['.']       # GenomicArrayOfSets -> ChromVector
-                             .array[al['start']:al['end']]          # ChromVector -> StepVector
-                             .get_steps(values_only=True))          # StepVector -> {features}
-                    # If an alignment does not map to a feature, an empty set is returned
-                    if len(match) != 0))
+            feat_matches = feat_matches.union(*(
+                    Features.chrom_vectors[al['chrom']]['.']  # GenomicArrayOfSets -> ChromVector
+                             .array[al['start']:al['end']]    # ChromVector -> StepVector
+                             .get_steps(values_only=True)))   # StepVector -> {features}
         except KeyError as ke:
             self.stats.chrom_misses[ke.args[0]] += 1
 
@@ -133,33 +131,45 @@ def choose(cls, candidates: Set[feature_record_tuple], alignment: dict) -> Mappi
             selections: a set of features which passed selection
         """
 
-        hits, min_rank = [], sys.maxsize
-
-        for feat, strand, matches in candidates:
-            for rule, rank, iv_match in matches:
-                if rank > min_rank: continue
-                if alignment not in iv_match: continue
-                if rank < min_rank: min_rank = rank
-                hits.append((rank, rule, feat, strand))
+        hits = [(rank, rule, feat, strand)
+                for feat, strand, matches in candidates
+                for rule, rank, iv_match in matches
+                if alignment in iv_match]
 
         if not hits: return {}
-
         selections = defaultdict(set)
-        for hit in hits:
-            if hit[0] != min_rank: continue
-            _, rule, feat, strand = hit
+        min_rank = min(hits, key=lambda x: x[0])
 
-            strand = (alignment['strand'], strand)
-            nt5end = alignment['nt5']
-            length = alignment['len']
+        for rank, rule, feat, strand in hits:
+            if rank != min_rank: continue
 
             rule_def = FeatureSelector.rules_table[rule]
-            if strand not in rule_def["Strand"]: continue
-            if nt5end not in rule_def["nt5end"]: continue
-            if length not in rule_def["Length"]: continue
+            if alignment['nt5end'] not in rule_def["nt5end"]: continue
+            if alignment['Length'] not in rule_def["Length"]: continue
+            if alignment['Strand'] ^ strand not in rule_def["Strand"]: continue
+            selections[feat].add(rule)
+
+        return selections
+
+    """
+    # MEGAZORD list comprehension??:
+        required = FeatureSelector.rules_table
+        min_rank = min(rank for _, _, matches in candidates for _, rank, _ in matches)
+        hits = [(rank, rule, feat)
+                 for feat, strand, matches in candidates
+                 for rule, rank, iv_match in matches
+                 if rank == min_rank
+                 if alignment in iv_match
+                 if alignment['nt5end'] in required[rule]['nt5end']
+                 if alignment['Length'] in required[rule]['Length']
+                 if (strand ^ alignment['Strand']) in required[rule]["Strand"]]
+
+        selections = defaultdict(set)
+        for rank, rule, feat in hits:
             selections[feat].add(rule)
 
         return selections
+    """
 
     @staticmethod
     def build_selectors(rules_table) -> List[dict]:
diff --git a/tiny/rna/counter/hts_parsing.py b/tiny/rna/counter/hts_parsing.py
index 5e991385..e1bb5eac 100644
--- a/tiny/rna/counter/hts_parsing.py
+++ b/tiny/rna/counter/hts_parsing.py
@@ -72,24 +72,24 @@ def _parse_alignments(self, file_obj) -> Iterator[dict]:
 
                 # Note: we assume sRNA sequencing data is NOT reversely stranded
                 if (int(cols[1]) & 16):
-                    strand = '-'
+                    strand = False  # -
                     try:
                         nt5 = complement[seq[-1]]
                     except KeyError:
                         nt5 = chr(seq[-1])
                 else:
-                    strand = '+'
+                    strand = True  # +
                     nt5 = chr(seq[0])
 
                 yield {
                     "name": cols[0].decode(),
-                    "len": length,
+                    "Length": length,
                     "seq": seq,
-                    "nt5": nt5,
+                    "nt5end": nt5,
                     "chrom": cols[2].decode(),
                     "start": start,
                     "end": start + length,
-                    "strand": strand
+                    "Strand": strand
                 }
         except Exception as e:
             # Append to error message while preserving exception provenance and traceback
@@ -548,7 +548,7 @@ def _finalize_features(self):
 
                 for sub_iv in merged_sub_ivs:
                     finalized_match_tuples = self.selector.build_interval_selectors(sub_iv, sorted_matches.copy())
-                    self.feats[sub_iv] += (tagged_id, sub_iv.strand, tuple(finalized_match_tuples))
+                    self.feats[sub_iv] += (tagged_id, sub_iv.strand == '+', tuple(finalized_match_tuples))
 
     @staticmethod
     def _merge_adjacent_subintervals(unmerged_sub_ivs: List[HTSeq.GenomicInterval]) -> list:
diff --git a/tiny/rna/counter/matching.py b/tiny/rna/counter/matching.py
index 67767aa5..a948ad7b 100644
--- a/tiny/rna/counter/matching.py
+++ b/tiny/rna/counter/matching.py
@@ -28,7 +28,7 @@ def __init__(self, strand):
         self.select = (self.strand == 'sense')
 
     def __contains__(self, x):
-        return self.select == (x[0] == x[1])
+        return self.select ^ x
 
     def __repr__(self): return str(self.strand)
 
diff --git a/tiny/rna/counter/statistics.py b/tiny/rna/counter/statistics.py
index d08249d8..1ac80d1c 100644
--- a/tiny/rna/counter/statistics.py
+++ b/tiny/rna/counter/statistics.py
@@ -42,7 +42,7 @@ def count_bundle(self, aln_bundle: iter) -> dict:
 
         bundle_read = aln_bundle[0]
         loci_counts = len(aln_bundle)
-        nt5, seqlen = bundle_read['nt5'], len(bundle_read['seq'])
+        nt5, seqlen = bundle_read['nt5end'], bundle_read['Length']
 
         # Calculate counts for multi-mapping
         read_counts = int(bundle_read['name'].split('=')[1])
@@ -477,18 +477,18 @@ def record_alignment_details(self, aln, bundle, assignments):
 
         # Perform reverse complement for anti-sense reads
         read = aln['seq'] \
-            if aln['strand'] == '+' \
+            if aln['Strand'] == '+' \
             else aln['seq'][::-1].translate(self.complement)
 
         # sequence, cor_counts, strand, start, end, feat1;feat2;feat3
-        self.alignments.append((read, bundle['corr_count'], aln['strand'], aln['start'], aln['end'],
+        self.alignments.append((read, bundle['corr_count'], aln['Strand'], aln['start'], aln['end'],
                                 ';'.join(assignments)))
 
     def record_diagnostics(self, assignments, n_candidates, aln, bundle):
         """Records basic diagnostic info"""
 
         if len(assignments) == 0:
-            if aln['strand'] == '+':
+            if aln['Strand'] == '+':
                 self.alignment_diags['Uncounted alignments (+)'] += 1
             else:
                 self.alignment_diags['Uncounted alignments (-)'] += 1

From 220bfb2191c033c3a645983e8f487e0dbc29e193 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sun, 14 Aug 2022 11:18:41 -0700
Subject: [PATCH 06/29] Native Python performance improvement:

By slightly adjusting the way case-insensitive dictionary entries are constructed, the construction time of these dictionaries has been substantially reduced which makes GFF parsing faster. During a few test runs I saw reductions in the ballpark of 50% for the GFF parsing stage.
---
 tiny/rna/counter/hts_parsing.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/tiny/rna/counter/hts_parsing.py b/tiny/rna/counter/hts_parsing.py
index e1bb5eac..f5a3ae79 100644
--- a/tiny/rna/counter/hts_parsing.py
+++ b/tiny/rna/counter/hts_parsing.py
@@ -228,13 +228,14 @@ def parse_GFF_attribute_string(attrStr, extra_return_first_value=False, gff_vers
 class CaseInsensitiveAttrs(Dict[str, tuple]):
     """A dictionary subclass that allows for case-insensitive queries against feature attributes"""
 
+    template = namedtuple("Entry", "orig_key orig_val ci_val")(None, None, None)
+
     def __init__(self):
         super().__init__()
-        self.Entry = namedtuple("Entry", "orig_key orig_val ci_val")
 
     def __setitem__(self, key: str, val: tuple):
         lowercase_val = tuple(v.lower() for v in val)
-        super().__setitem__(key.lower(), self.Entry(key, val, lowercase_val))
+        super().__setitem__(key.lower(), self.template._replace(orig_key=key, orig_val=val, ci_val=lowercase_val))
 
     def __getitem__(self, key: str):
         # Allows case-insensitive key lookups which return original case values

From f6b0f925e578499e00871a7349ac8c1b55471e08 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sun, 14 Aug 2022 21:36:08 -0700
Subject: [PATCH 07/29] Bugfix

---
 tiny/rna/counter/features.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tiny/rna/counter/features.py b/tiny/rna/counter/features.py
index ee43f0d5..5ba05033 100644
--- a/tiny/rna/counter/features.py
+++ b/tiny/rna/counter/features.py
@@ -138,7 +138,7 @@ def choose(cls, candidates: Set[feature_record_tuple], alignment: dict) -> Mappi
 
         if not hits: return {}
         selections = defaultdict(set)
-        min_rank = min(hits, key=lambda x: x[0])
+        min_rank = min(hits, key=lambda x: x[0])[0]
 
         for rank, rule, feat, strand in hits:
             if rank != min_rank: continue

From 8f2c0378f971b462d28cf70aaa0b29c90c5d9ed3 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Mon, 22 Aug 2022 16:59:59 -0700
Subject: [PATCH 08/29] Refactored the StepVector's core C++ so that it is a
 more proper definition of a templated class. Cython doesn't particularly
 care, but this is useful for C++ to C++ direct testing for easier debugging.
 This has also led to some much needed improvements to the PyRef wrapper for
 PyObjects. This refactoring has also fixed a major issue with the StepVector
 following recent changes which caused massive accumulations of features. It
 has also led to a slight reduction in memory.

At the end of the day, the procedure and design of our specialized Cython StepVector has been substantially improved.
---
 tiny/rna/counter/hts_parsing.py               |  14 +-
 tiny/rna/counter/stepvector/_stepvector.pxd   |   3 -
 tiny/rna/counter/stepvector/src/PyRef.h       |  84 +++++--
 .../rna/counter/stepvector/src/StepVector.cpp | 219 ------------------
 tiny/rna/counter/stepvector/src/StepVector.h  | 173 ++++++++++++++
 5 files changed, 243 insertions(+), 250 deletions(-)
 delete mode 100644 tiny/rna/counter/stepvector/src/StepVector.cpp

diff --git a/tiny/rna/counter/hts_parsing.py b/tiny/rna/counter/hts_parsing.py
index f5a3ae79..7eb187c5 100644
--- a/tiny/rna/counter/hts_parsing.py
+++ b/tiny/rna/counter/hts_parsing.py
@@ -318,10 +318,6 @@ def not_implemented(self):
 StepVector = HTSeq.GenomicArrayOfSets
 Tags = DefaultDict[str, Set[str]]
 
-use_cython_stepvector = True
-if use_cython_stepvector:
-    from tiny.rna.counter.stepvector import StepVector
-    setattr(HTSeq.StepVector, 'StepVector', StepVector)
 
 class ReferenceTables:
     """A GFF parser which builds feature, alias, and class reference tables
@@ -350,13 +346,15 @@ class ReferenceTables:
     source_filter = []
     type_filter = []
 
-    def __init__(self, gff_files: Dict[str, list], feature_selector, **kwargs):
-        self.all_features = kwargs.get('all_features', False)
+    def __init__(self, gff_files: Dict[str, list], feature_selector, **prefs):
+        self.all_features = prefs.get('all_features', False)
         self.selector = feature_selector
-        self._set_filters(**kwargs)
+        self._set_filters(**prefs)
         self.gff_files = gff_files
         # ----------------------------------------------------------- Primary Key:
-        if use_cython_stepvector:
+        if prefs['step_vector'] == 'Cython':
+            from tiny.rna.counter.stepvector import StepVector
+            setattr(HTSeq.StepVector, 'StepVector', StepVector)
             self.feats = HTSeq.GenomicArray("auto", stranded=False)         # Root Match ID
         else:
             self.feats = HTSeq.GenomicArrayOfSets("auto", stranded=False)   # Root Match ID
diff --git a/tiny/rna/counter/stepvector/_stepvector.pxd b/tiny/rna/counter/stepvector/_stepvector.pxd
index df485bd9..daccea6a 100644
--- a/tiny/rna/counter/stepvector/_stepvector.pxd
+++ b/tiny/rna/counter/stepvector/_stepvector.pxd
@@ -13,9 +13,6 @@ cdef extern from "src/PyRef.h" namespace "PyPtr":
         PyObject* get() const
         PyRef& operator+(const PyRef &po)
 
-cdef extern from "src/StepVector.cpp":
-    pass
-
 cdef extern from "src/StepVector.h" namespace "sparse_vectors":
     cdef cppclass _StepVector[T]:
         ctypedef ccmap[long int, T].const_iterator const_iterator
diff --git a/tiny/rna/counter/stepvector/src/PyRef.h b/tiny/rna/counter/stepvector/src/PyRef.h
index 37014b28..3458d649 100644
--- a/tiny/rna/counter/stepvector/src/PyRef.h
+++ b/tiny/rna/counter/stepvector/src/PyRef.h
@@ -1,30 +1,38 @@
 #include "Python.h"
 #include <iostream>
+#include <cstring>
 
 namespace PyPtr {
     class PyRef {
         PyObject* obj;
+        bool debug = false;
 
         public:
             PyObject* get() const {return obj;}
 
             // Default constructor
             PyRef() {
-                obj = NULL;
+                obj = PySet_New(NULL);
             }
 
             // Obj constructor
-            PyRef(PyObject* obj) {
-                if (PySet_Check(obj)){
-                    this->obj = obj;
+            PyRef(PyObject* payload) {
+                if (PySet_Check(payload)){
+                    obj = payload;
+                    Py_XINCREF(obj);
                 } else {
                     // PySet_New treats the argument as an iterable
                     // We don't want that, e.g. if adding a tuple
                     // PySet_Add simply adds without iteration
-                    this->obj = PySet_New(NULL);
-                    PySet_Add(this->obj, obj);
+                    obj = PySet_New(NULL);
+                    PySet_Add(obj, payload);
+                }
+
+                if (debug){
+                    std::cout << "Object ctor: ";
+                    PyObject_Print(payload, stdout, 0);
+                    std::cout << " (obj: " << obj << ")" << std::endl;
                 }
-                Py_XINCREF(this->obj);
             }
 
             // Destructor
@@ -35,50 +43,86 @@ namespace PyPtr {
             // Copy constructor
             PyRef(const PyRef& other) {
                 obj = PySet_New(other.obj);
-                Py_XINCREF(obj);
-                Py_XDECREF(other.obj);
+
+                if (debug) {
+                    std::cout << "Copy ctor: ";
+                    PyObject_Print(other.obj, stdout, 0);
+                    std::cout << " (obj: " << other.obj << " -> " << obj << ")";
+                    std::cout << std::endl << std::flush;
+                }
             }
 
             // Move constructor
             PyRef(PyRef&& other) {
+                if (debug) {
+                    std::cout << "Move ctor: ";
+                    PyObject_Print(other.obj, stdout, 0);
+                    std::cout << " (obj: " << other.obj << ")";
+                    std::cout << std::endl << std::flush;
+                }
+
                 obj = other.obj;
                 Py_XDECREF(other.obj);
             }
 
             // Assignment
             PyRef& operator=(const PyRef& other) {
+                if (debug) {
+                    std::cout << "Assignment: ";
+                    PyObject_Print(other.obj, stdout, 0);
+                    std::cout << " (obj: " << other.obj << ")";
+                    std::cout << std::endl << std::flush;
+                }
+
                 Py_XDECREF(obj);
-                obj = other.obj;
-                Py_XINCREF(obj);
+                obj = PySet_New(other.obj);
                 return *this;
             }
 
             // Move assignment
             PyRef& operator=(PyRef&& other) {
+                if (debug) {
+                    std::cout << "Move assignment: ";
+                    PyObject_Print(other.obj, stdout, 0);
+                    std::cout << " (obj: " << other.obj << ")";
+                    std::cout << std::endl << std::flush;
+                }
+
                 Py_XDECREF(obj);
-                obj = PySet_New(other.obj);
-                Py_XINCREF(obj);
+                obj = other.obj;
+                // Py_XINCREF(obj);
                 other.obj = NULL;
                 return *this;
             }
 
             PyRef& operator+= (const PyRef& other) {
+                if (debug) {
+                    std::cout << "+=" << std::endl;
+                }
+
                 if (PySet_Check(other.obj)){
-                    _PySet_Update(this->obj, PyObject_GetIter(other.obj));
+                    _PySet_Update(obj, PyObject_GetIter(other.obj));
                 } else {
-                    PySet_Add(this->obj, other.obj);
+                    std::cerr << "Error: rhs value holds a non-set type PyObject." << std::endl;
                 }
                 return *this;
             }
 
-            PyRef operator+ (const PyRef& other) {
+            PyRef operator+ (const PyRef& rhs) {
+                if (debug){
+                    PyObject_Print(obj, stdout, 0);
+                    std::cout << " + ";
+                    PyObject_Print(rhs.obj, stdout, 0);
+                    std::cout << std::endl;
+                }
+
                 PyRef result(obj);
-                if (PySet_Check(other.obj)){
-                    _PySet_Update(result.obj, PyObject_GetIter(other.obj));
+                if (PySet_Check(rhs.obj)){
+                    _PySet_Update(result.obj, PyObject_GetIter(rhs.obj));
                 } else {
-                    PySet_Add(result.obj, other.obj);
+                    std::cerr << "Error: rhs value holds a non-set type PyObject." << std::endl;
                 }
-                Py_XINCREF(result.obj);
+                
                 return result;
             }
 
diff --git a/tiny/rna/counter/stepvector/src/StepVector.cpp b/tiny/rna/counter/stepvector/src/StepVector.cpp
deleted file mode 100644
index f07ca296..00000000
--- a/tiny/rna/counter/stepvector/src/StepVector.cpp
+++ /dev/null
@@ -1,219 +0,0 @@
-#include "StepVector.h"
-
-using namespace sparse_vectors;
-
-template <class T> _StepVector<T>::_StepVector() { m[min_index] = T(); }
-
-template <class T> const long int _StepVector<T>::min_index = LONG_MIN;
-
-template <class T> const long int _StepVector<T>::max_index = LONG_MAX;
-
-template <class T> const T _StepVector<T>::operator[](long int i) const {
-    const_iterator it = m.upper_bound(i);
-    it--;
-    return it->second;
-}
-
-template <class T>
-void _StepVector<T>::set_value(long int from, long int to, T value) {
-    if (from > to)
-        throw std::out_of_range("Indices reversed in StepVector.");
-
-    // Unless the new step extends to the end, we need to insert a new
-    // value afterwards unless the step to the right has the same value
-    if (to < max_index) {
-        T next_value = (*this)[to + 1];
-        if (!(next_value == value))
-            m[to + 1] = next_value;
-    }
-
-    // Find the left step, i.e., the step whose start is smaller or equal
-    // to 'from':
-    typename std::map<long int, T>::iterator left = m.upper_bound(from);
-    left--;
-    assert(left->first <= from);
-
-    // Get rid of the steps present between from and to
-    typename std::map<long int, T>::iterator it = m.lower_bound(from);
-    if (it->first == from)
-        it++;
-    assert(it->first > from);
-    if (it->first <= to) {
-        m.erase(it, m.upper_bound(to));
-    }
-
-    if (!(left->second == value)) {
-        if (left->first != from)
-            // Insert a new step
-            m[from] = value;
-        else {
-            // We have from == left->first, so the step is already present.
-            // Would changing m[from] to value make it equal to its left
-            // neighbor?
-            if (left == m.begin())
-                // no, there is no left neighbor
-                m[from] = value;
-            else {
-                typename std::map<long int, T>::iterator leftleft = left;
-                leftleft--;
-                if (!(leftleft->second == value))
-                    // ok, change the value
-                    m[from] = value;
-                else
-                    // no, rather delete the step
-                    m.erase(left);
-            }
-        }
-    }
-}
-
-bool debug = false;
-template <class T>
-void _StepVector<T>::add_value(long int from, long int to, T value) {
-    if (debug) {
-        std::cout << std::endl << "Begin: " << std::flush;
-        PyObject_Print(value.get(), stdout, 0);
-        std::cout << std::endl << std::flush;
-    }
-    if (from > to)
-        throw std::out_of_range("Indices reversed in StepVector.");
-
-    if (to < max_index) {
-        T next_value = (*this)[to + 1];
-        auto before = m[to + 1];
-        m[to + 1] = next_value;
-        if (debug) {
-            std::cout << to + 1 << ": setting \"next\" from: ";
-            PyObject_Print(before.get(), stdout, 0);
-            std::cout << " to ";
-            PyObject_Print(m[to + 1].get(), stdout, 0);
-            std::cout << " (" << m[to+1].get() << ") " << std::endl;
-        }
-    }
-
-    typename std::map<long int, T>::iterator it = m.upper_bound(from);
-    it--;
-    bool need_to_insert_step_at_from = it->first < from;
-    T old_val_at_from;
-    if (need_to_insert_step_at_from) {
-        old_val_at_from = it->second;
-        it++;
-    }
-    // Now, it points to the first element with it->first >= from
-
-    for (; it != m.end() && it->first <= to; it++){
-        if (debug){
-            std::cout << it->first << ": adding to ";
-            PyObject_Print(it->second.get(), stdout, Py_PRINT_RAW);
-            std::cout << " (" << it->second.get() << ") " << std::endl;
-        }
-
-        it->second += value;
-    }
-
-    if (need_to_insert_step_at_from){
-        m[from] = old_val_at_from + value;
-        if (debug){
-            std::cout << from << ": inserting step into ";
-            PyObject_Print(old_val_at_from.get(), stdout, Py_PRINT_RAW);
-            std::cout << " (" << old_val_at_from.get() << ") " << std::endl;
-        }
-    }
-}
-
-template <class T>
-void _StepVector<T>::apply_to_values(long int from, long int to, void (*func)(T &val)) {
-    if (from > to)
-        throw std::out_of_range("Indices reversed in StepVector.");
-
-    if (to < max_index) {
-        T next_value = (*this)[to + 1];
-        m[to + 1] = next_value;
-    }
-
-    typename std::map<long int, T>::iterator it = m.upper_bound(from);
-    it--;
-    bool need_to_insert_step_at_from = it->first < from;
-    T old_val_at_from;
-    if (need_to_insert_step_at_from) {
-        old_val_at_from = it->second;
-        it++;
-    }
-    // Now, it points to the first element with it->first >= from
-
-    for (; it != m.end() && it->first <= to; it++)
-        func(it->second);
-
-    if (need_to_insert_step_at_from) {
-        func(old_val_at_from);
-        m[from] = old_val_at_from;
-    }
-}
-
-template <class T>
-typename _StepVector<T>::const_iterator
-_StepVector<T>::get_values(long int from) const {
-    return --m.upper_bound(from);
-}
-
-template< class T >
-long int _StepVector<T>::num_values( ) const{
-  return this->m.size();
-}
-
-template <class T>
-typename _StepVector<T>::const_iterator
-_StepVector<T>::begin() const {
-    return m.begin();
-}
-
-template <class T>
-typename _StepVector<T>::const_iterator
-_StepVector<T>::end() const {
-    return m.end();
-}
-
-//template<class T>
-//iterator::iterator(){
-//    current = m.begin()
-//    last = m.end()
-//}
-//
-//template<class T>
-//iterator::iterator(typename const_iterator from){
-//    current = from
-//    last = m.end()
-//}
-//
-//template<class T>
-//std::pair<long int, T>& iterator::operator*(){return current;}
-//
-//template<class T>
-//iterator iterator::operator++(){
-//    if (current == last){
-//        PyErr_SetString(PyExc_StopIteration, "Reached StepVector end");
-//        return NULL;
-//    } else {
-//        return *current++;
-//    }
-//}
-//
-//template<class T>
-//iterator iterator::operator--(){
-//    if (current == begin()){
-//        PyErr_SetString(PyExc_StopIteration, "Reached StepVector start");}
-//        return NULL;
-//    } else {
-//        return *current--;
-//    }
-//}
-//
-//template<class T>
-//bool iterator::operator==(const iterator other){
-//    return current == other.current;
-//}
-//
-//template<class T>
-//bool iterator::operator!=(const iterator other){
-//    return current != other.current;
-//}
\ No newline at end of file
diff --git a/tiny/rna/counter/stepvector/src/StepVector.h b/tiny/rna/counter/stepvector/src/StepVector.h
index ee64a316..09225ef3 100644
--- a/tiny/rna/counter/stepvector/src/StepVector.h
+++ b/tiny/rna/counter/stepvector/src/StepVector.h
@@ -27,6 +27,179 @@ namespace sparse_vectors {
             const_iterator begin( ) const;
             const_iterator end( ) const;
     };
+
+    template <class T> _StepVector<T>::_StepVector() { 
+        m[min_index] = T(); 
+    }
+
+    template <class T> const long int _StepVector<T>::min_index = LONG_MIN;
+
+    template <class T> const long int _StepVector<T>::max_index = LONG_MAX;
+
+    template <class T> const T _StepVector<T>::operator[](long int i) const {
+        const_iterator it = m.upper_bound(i);
+        it--;
+        return it->second;
+    }
+
+    template <class T>
+    void _StepVector<T>::set_value(long int from, long int to, T value) {
+        if (from > to)
+            throw std::out_of_range("Indices reversed in StepVector.");
+
+        // Unless the new step extends to the end, we need to insert a new
+        // value afterwards unless the step to the right has the same value
+        if (to < max_index) {
+            T next_value = (*this)[to + 1];
+            if (!(next_value == value))
+                m[to + 1] = next_value;
+        }
+
+        // Find the left step, i.e., the step whose start is smaller or equal
+        // to 'from':
+        typename std::map<long int, T>::iterator left = m.upper_bound(from);
+        left--;
+        assert(left->first <= from);
+
+        // Get rid of the steps present between from and to
+        typename std::map<long int, T>::iterator it = m.lower_bound(from);
+        if (it->first == from)
+            it++;
+        assert(it->first > from);
+        if (it->first <= to) {
+            m.erase(it, m.upper_bound(to));
+        }
+
+        if (!(left->second == value)) {
+            if (left->first != from)
+                // Insert a new step
+                m[from] = value;
+            else {
+                // We have from == left->first, so the step is already present.
+                // Would changing m[from] to value make it equal to its left
+                // neighbor?
+                if (left == m.begin())
+                    // no, there is no left neighbor
+                    m[from] = value;
+                else {
+                    typename std::map<long int, T>::iterator leftleft = left;
+                    leftleft--;
+                    if (!(leftleft->second == value))
+                        // ok, change the value
+                        m[from] = value;
+                    else
+                        // no, rather delete the step
+                        m.erase(left);
+                }
+            }
+        }
+    }
+
+    bool debug = false;
+    template <class T>
+    void _StepVector<T>::add_value(long int from, long int to, T value) {
+        if (debug) {
+            std::cout << std::endl << "Begin: " << std::flush;
+            PyObject_Print(value.get(), stdout, 0);
+            std::cout << std::endl << std::flush;
+        }
+        if (from > to)
+            throw std::out_of_range("Indices reversed in StepVector.");
+
+        if (to < max_index) {
+            T next_value = (*this)[to + 1];     // copy ctor
+            auto before = m[to + 1];            // copy ctor
+            m[to + 1] = next_value;             // assignment operator
+            if (debug) {
+                std::cout << to + 1 << ": setting \"next\" from: ";
+                PyObject_Print(before.get(), stdout, 0);
+                std::cout << " (" << before.get() << ") to ";
+                PyObject_Print(m[to + 1].get(), stdout, 0);
+                std::cout << " (" << m[to+1].get() << ") " << std::endl;
+            }
+        }
+
+        typename std::map<long int, T>::iterator it = m.upper_bound(from);
+        it--;
+        bool need_to_insert_step_at_from = it->first < from;
+        T old_val_at_from;
+        if (need_to_insert_step_at_from) {
+            old_val_at_from = it->second;       // assignment operator
+            it++;
+        }
+        // Now, it points to the first element with it->first >= from
+
+        for (; it != m.end() && it->first <= to; it++){
+            if (debug){
+                std::cout << it->first << ": adding to ";
+                PyObject_Print(it->second.get(), stdout, Py_PRINT_RAW);
+                std::cout << " (" << it->second.get() << ") " << std::endl;
+            }
+
+            it->second += value;
+        }
+
+        if (need_to_insert_step_at_from){
+            m[from] = old_val_at_from + value;  // + operator and move assignment operator
+            if (debug){
+                std::cout << from << ": inserting step into ";
+                PyObject_Print(old_val_at_from.get(), stdout, Py_PRINT_RAW);
+                std::cout << " (" << old_val_at_from.get() << ") " << std::endl;
+            }
+        }
+    }
+
+    template <class T>
+    void _StepVector<T>::apply_to_values(long int from, long int to, void (*func)(T &val)) {
+        if (from > to)
+            throw std::out_of_range("Indices reversed in StepVector.");
+
+        if (to < max_index) {
+            T next_value = (*this)[to + 1];
+            m[to + 1] = next_value;
+        }
+
+        typename std::map<long int, T>::iterator it = m.upper_bound(from);
+        it--;
+        bool need_to_insert_step_at_from = it->first < from;
+        T old_val_at_from;
+        if (need_to_insert_step_at_from) {
+            old_val_at_from = it->second;
+            it++;
+        }
+        // Now, it points to the first element with it->first >= from
+
+        for (; it != m.end() && it->first <= to; it++)
+            func(it->second);
+
+        if (need_to_insert_step_at_from) {
+            func(old_val_at_from);
+            m[from] = old_val_at_from;
+        }
+    }
+
+    template <class T>
+    typename _StepVector<T>::const_iterator
+    _StepVector<T>::get_values(long int from) const {
+        return --m.upper_bound(from);
+    }
+
+    template< class T >
+    long int _StepVector<T>::num_values( ) const{
+    return this->m.size();
+    }
+
+    template <class T>
+    typename _StepVector<T>::const_iterator
+    _StepVector<T>::begin() const {
+        return m.begin();
+    }
+
+    template <class T>
+    typename _StepVector<T>::const_iterator
+    _StepVector<T>::end() const {
+        return m.end();
+    }
 };
 
 #endif //_STEP_VECTOR_H_
\ No newline at end of file

From c09d1cb33ad8603bf59129e4d01101cd664ade12 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Mon, 22 Aug 2022 17:11:09 -0700
Subject: [PATCH 09/29] Refactored CaseInsensitiveDict to use regular tuples
 for internally storing keys/values rather than NamedTuples. The overhead for
 the convenience of having named indices was far too high, and definitely not
 worth it for this particular feature

---
 tiny/rna/counter/hts_parsing.py | 42 ++++++++++++++++++++++-----------
 1 file changed, 28 insertions(+), 14 deletions(-)

diff --git a/tiny/rna/counter/hts_parsing.py b/tiny/rna/counter/hts_parsing.py
index 7eb187c5..b65cecd4 100644
--- a/tiny/rna/counter/hts_parsing.py
+++ b/tiny/rna/counter/hts_parsing.py
@@ -3,7 +3,7 @@
 import sys
 import re
 
-from collections import Counter, defaultdict, namedtuple
+from collections import Counter, defaultdict
 from typing import Tuple, List, Dict, Iterator, Optional, DefaultDict, Set, Union
 from inspect import stack
 
@@ -226,22 +226,36 @@ def parse_GFF_attribute_string(attrStr, extra_return_first_value=False, gff_vers
 
 
 class CaseInsensitiveAttrs(Dict[str, tuple]):
-    """A dictionary subclass that allows for case-insensitive queries against feature attributes"""
-
-    template = namedtuple("Entry", "orig_key orig_val ci_val")(None, None, None)
+    """A dictionary subclass that allows for case-insensitive queries against feature attributes
+
+    From a bird's eye view, this class holds the feature attribute's name as the key,
+    and a tuple of values associated with that attribute name. The attribute's values did
+    not contain any commas, this tuple will have a length of 1. Otherwise, the original value
+    is tokenized on comma and each token is stored in a separate tuple index.
+
+    Internally, each key is stored in lowercase form, and its associated value is a (nested) tuple
+    that contains (at the following indices):
+        [0]: The key (attribute name) in its original case
+        [1]: A tuple of values in their original case
+        [2]: A tuple of values in lowercase form
+
+    Interactions with the Dict base class involve handling the "internal" nested tuple described
+    above. Functions which call self[item] in turn call these methods, and therefore the handling of the
+    internal tuple is abstracted away; these functions only deal with the key/values in their original form.
+    """
 
     def __init__(self):
         super().__init__()
 
-    def __setitem__(self, key: str, val: tuple):
-        lowercase_val = tuple(v.lower() for v in val)
-        super().__setitem__(key.lower(), self.template._replace(orig_key=key, orig_val=val, ci_val=lowercase_val))
+    def __setitem__(self, key: str, vals: tuple):
+        lowercase_vals = tuple(v.lower() for v in vals)
+        super().__setitem__(key.lower(), (key, vals, lowercase_vals))
 
     def __getitem__(self, key: str):
         # Allows case-insensitive key lookups which return original case values
         # Ensure that KeyError contains the original key
         if key.lower() not in self: raise KeyError(key)
-        return super().__getitem__(key.lower()).orig_val
+        return super().__getitem__(key.lower())[1]
 
     def __contains__(self, key: str):
         # Allows case-insensitive membership queries by key
@@ -249,11 +263,11 @@ def __contains__(self, key: str):
 
     def __str__(self):
         # Returns original case keys/values
-        return str({v.orig_key: v.orig_val for v in super().values()})
+        return str({v[0]: v[1] for v in super().values()})
 
     def __repr__(self):
         # Returns both original case and lowercase keys/values
-        return str({f"{k}/{v.orig_key}": f"{v.ci_val}/{v.orig_val}" for k,v in super().items()})
+        return str({f"{k}/{v[0]}": f"{v[2]}/{v[1]}" for k,v in super().items()})
 
     def setdefault(self, key: str, value: Optional[Tuple]=None):
         if key not in self:
@@ -269,12 +283,12 @@ def get(self, key: str, default=None):
     def keys(self):
         # Roughly mimics a KeysView with original case
         for v in super(CaseInsensitiveAttrs, self).values():
-            yield v.orig_key
+            yield v[0]
 
     def values(self):
         # Roughly mimics a ValuesView with original case
         for v in super(CaseInsensitiveAttrs, self).values():
-            yield v.orig_val
+            yield v[1]
 
     def items(self):
         # Roughly mimics an ItemsView with original case
@@ -295,12 +309,12 @@ def contains_ident(self, query: Tuple[Union[str, Wildcard], Union[str, Wildcard]
         if key_type is val_type is str:
             # Allows case-insensitive membership queries by (key, value)
             return key in self and \
-                   val in super(CaseInsensitiveAttrs, self).__getitem__(key).ci_val
+                   val in super(CaseInsensitiveAttrs, self).__getitem__(key)[2]
         if key_type is str and val_type is Wildcard:
             return key in self
         if key_type is Wildcard and val_type is str:
             for v in super(CaseInsensitiveAttrs, self).values():
-                if val in v.ci_val: return True
+                if val in v[2]: return True
             else: return False
 
     # Dict methods not implemented which are invalid if delegated to dict class

From 5593853d08eabc29a288d29042a3563410f74514 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Mon, 22 Aug 2022 17:22:41 -0700
Subject: [PATCH 10/29] counter.py: added a commandline option to allow users
 to choose between our Cython or HTSeq's StepVector.

setup.py: refactored args for Cython.Extension, added '-O3', and added an extension entry for test_stepvec.pyx

_stepvector.pyx: misc. improvements
---
 setup.py                                    | 18 +++++++++++++++---
 tiny/rna/counter/counter.py                 |  2 ++
 tiny/rna/counter/stepvector/_stepvector.pyx |  8 ++++----
 3 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/setup.py b/setup.py
index cc79fd94..b3e03fab 100644
--- a/setup.py
+++ b/setup.py
@@ -30,13 +30,25 @@ def in_conda_env(self):
         return all([os.getenv(conda_var) for conda_var in ["CONDA_PREFIX", "CONDA_DEFAULT_ENV"]])
 
 debug_cython = False
+cxx_extension_args = {
+    'extra_compile_args': [
+        '-isystem', '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include',
+        '-stdlib=libc++', '-std=c++11',
+        '-O3'],
+    'extra_link_args': ['-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib'],
+    'language': 'c++'
+}
 cython_extensions = [
     setuptools.Extension(
         "tiny.rna.counter.stepvector._stepvector",
         sources=['tiny/rna/counter/stepvector/_stepvector.pyx'],
-        extra_compile_args=['-isystem', '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include', '-stdlib=libc++', '-std=c++11'],
-        extra_link_args=['-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib'],
-        language='c++')
+        **cxx_extension_args
+    ),
+    setuptools.Extension(
+        "tiny.rna.counter.stepvector.test_stepvec",
+        sources=['tiny/rna/counter/stepvector/test_stepvec.pyx'],
+        **cxx_extension_args
+    )
 ]
 
 setuptools.setup(
diff --git a/tiny/rna/counter/counter.py b/tiny/rna/counter/counter.py
index 7733907e..f84fe926 100644
--- a/tiny/rna/counter/counter.py
+++ b/tiny/rna/counter/counter.py
@@ -60,6 +60,8 @@ def get_args():
     optional_args.add_argument('-d', '--report-diags', action='store_true',
                                help='Produce diagnostic information about uncounted/eliminated '
                                     'selection elements.')
+    optional_args.add_argument('-sv', '--step-vector', choices=['Cython', 'HTSeq'], default='Cython',
+                               help='Select which StepVector is used for interval -> feature resolution.')
 
     args = arg_parser.parse_args()
     setattr(args, 'normalize_by_hits', args.normalize_by_hits.lower() in ['t', 'true'])
diff --git a/tiny/rna/counter/stepvector/_stepvector.pyx b/tiny/rna/counter/stepvector/_stepvector.pyx
index 47f30f8a..59807f10 100644
--- a/tiny/rna/counter/stepvector/_stepvector.pyx
+++ b/tiny/rna/counter/stepvector/_stepvector.pyx
@@ -132,9 +132,8 @@ cdef class StepVector:
             stop_s = "inf"
         else:
             stop_s = str(self.stop)
-        return "<%s object, type '%s', index range %s:%s, %d step(s)>" % (
-            self.__class__.__name__, self.typecode(), start_s,
-            stop_s, self.num_steps())
+        return "<tinyRNA Cythonized %s object, index range %s:%s, %d step(s)>" % (
+            self.__class__.__name__, start_s, stop_s, self.num_steps())
 
     def typecode(self):
         return chr(self._typecode)
@@ -168,7 +167,8 @@ cdef class StepVector:
 
     # Todo
     def __eq__(self, other): pass
-    def __reduce__(self): pass
+    def __reduce__(self):
+        print("The __reduce__() function is not yet implemented")
     def apply(self, func, start=None, stop=None): pass
 
     @property

From 78180d92ce861c294ae45f26eb28f725c1523612 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Mon, 22 Aug 2022 17:23:01 -0700
Subject: [PATCH 11/29] Added _chromvector.pyx and test_stepvec.pyx

---
 tiny/rna/counter/stepvector/_chromvector.pyx | 259 +++++++++++++++++++
 tiny/rna/counter/stepvector/test_stepvec.pyx |  32 +++
 2 files changed, 291 insertions(+)
 create mode 100644 tiny/rna/counter/stepvector/_chromvector.pyx
 create mode 100644 tiny/rna/counter/stepvector/test_stepvec.pyx

diff --git a/tiny/rna/counter/stepvector/_chromvector.pyx b/tiny/rna/counter/stepvector/_chromvector.pyx
new file mode 100644
index 00000000..e0429fe5
--- /dev/null
+++ b/tiny/rna/counter/stepvector/_chromvector.pyx
@@ -0,0 +1,259 @@
+from ._stepvector import StepVector
+from HTSeq._HTSeq import GenomicInterval
+
+cdef class ChromVector(object):
+    """Counting vector covering a chromosome.
+
+    This class supports only the tinyRNA Cython implementation of the
+    HTSeq StepVector
+    """
+
+    cdef public object array
+    cdef public GenomicInterval iv
+    cdef public int offset
+    cdef public bint is_vector_of_sets
+    cdef public str _storage
+    cdef public str typecode
+    cdef public str memmap_dir
+
+    @classmethod
+    def create(cls, GenomicInterval iv, str typecode, str storage, str memmap_dir=""):
+        """Create ChromVector from GenomicInterval
+
+        Args:
+            iv (GenomicInterval): A GenomicInterval describing the chromosome
+              vector.
+            typecode ('d', 'i', 'l', 'b', or 'O'): What kind of data will be
+              stored inside this chromosome vector. 'd' for double, 'i' for int,
+              'l' for long int, 'b' for boolean, 'O' for arbitrary objects
+              (e.g. sets).
+            storage ('step', 'ndarray', or 'memmap'): What kind of storage to
+              use. 'ndarray' is appropriate for short chromosomes and stores
+              each position in the genome into memory. 'memmap' stores all
+              positions, but maps the memory onto disk for larger chromosomes.
+              'step' is a sparse representation similar to CSR matrices whereby
+              only the boundaries between genomic stretches with differing
+              data content are stored - see HTSeq.StepVector.
+            memmap_dir (str): If using 'memmap' storage, what folder to store
+              the memory maps. These can get quite big.
+
+        Returns:
+            An instance of ChromVector with the requested options.
+
+        """
+        ncv = cls()
+        ncv.iv = iv
+        ncv.array = StepVector.create()
+
+        ncv._storage = storage
+        ncv.typecode = typecode
+        # NOTE: As long as autochromosomes in GenomicArray are infinite length
+        # this has pretty limited use, but that might change
+        ncv.offset = iv.start
+        ncv.is_vector_of_sets = False
+        ncv.memmap_dir = memmap_dir
+        return ncv
+
+    @classmethod
+    def _create_view(cls, ChromVector vec, GenomicInterval iv):
+        if iv.length == 0:
+            raise IndexError("Cannot subset to zero-length interval.")
+        v = cls()
+        v.iv = iv
+        v.array = vec.array
+        v.offset = vec.offset
+        v.is_vector_of_sets = vec.is_vector_of_sets
+        v._storage = vec._storage
+        return v
+
+    def extend_to_include(self, iv):
+        if iv.strand != self.iv.strand:
+            raise ValueError(
+                'The new interval must match the current strandedness',
+            )
+
+        # Step 1: extend the interval
+        length = self.iv.length
+        startdiff = max(self.iv.start - iv.start, 0)
+        self.iv.extend_to_include(iv)
+        self.offset = self.iv.start
+
+        # Step 2: extend the array if needed, and shift-copy the old values
+        if self._storage == 'ndarray':
+            if self.typecode != 'O':
+                array = numpy.zeros(shape=(self.iv.length,), dtype=self.typecode)
+            else:
+                array = numpy.empty(shape=(self.iv.length,), dtype=self.typecode)
+                array[:] = None
+            array[startdiff: startdiff + length] = self.array[:]
+        elif self._storage == 'memmap':
+            array = numpy.memmap(
+                shape=(self.iv.length,), dtype=self.typecode,
+                filename=os.path.join(
+                    self.memmap_dir,
+                    self.iv.chrom + self.iv.strand + str(self.iv.start) + '_' \
+                        + str(self.iv.length) + ".nmm"),
+                mode='w+',
+            )
+            array[startdiff: startdiff + length] = self.array[:]
+        else:
+            # The StepVector is created in ChromVector.create without explicit
+            # boundaries, so it's already bound by 0, +inf. So we do not need
+            # to extend it here, but rather just set the slice to the right
+            # value
+            array = self.array
+        self.array = array
+
+    def __getitem__(self, index):
+        """Index or slice the chromosome.
+
+        The index can be a few things:
+        - an integer: get the value of the vector at that chromosome coordinate
+        - a 1-step slice e.g "4:7": get a view of the chromosome region
+          between those coordinates. The array data are not copied.
+        - a GenomicInterval: similar to slices, with the additional choice of
+          strandedness. If this argument is stranded but the chromosome itself
+          is not stranded, a nonstranded view of the chromosome region is
+          returned.
+
+        """
+        cdef slice index_slice
+        cdef long int index_int
+        cdef long int start, stop
+        cdef GenomicInterval iv
+
+        if isinstance(index, int):
+            index_int = index
+            if index_int < self.iv.start or index_int >= self.iv.end:
+                raise IndexError
+            return self.array[index_int - self.offset]
+
+        elif isinstance(index, slice):
+            index_slice = index
+            if index_slice.start is None:
+                start = self.iv.start
+            else:
+                start = index_slice.start
+                if start < self.iv.start:
+                    raise IndexError("start too small")
+
+            if index_slice.stop is None:
+                stop = self.iv.end
+            else:
+                stop = index_slice.stop
+                if stop > self.iv.end:
+                    raise IndexError("stop too large")
+
+            iv = GenomicInterval(self.iv.chrom, start, stop, self.iv.strand)
+
+            if not self.iv.contains(iv):
+                raise IndexError
+            return ChromVector._create_view(self, iv)
+
+        elif isinstance(index, GenomicInterval):
+            if not self.iv.contains(index):
+                raise IndexError
+
+            if self.iv.strand is strand_nostrand and \
+                    index.strand is not strand_nostrand:
+                iv = index.copy()   # Is this correct now?
+                iv.strand = strand_nostrand
+            else:
+                iv = index
+
+            return ChromVector._create_view(self, iv)
+
+        else:
+            raise TypeError("Illegal index type")
+
+    def __setitem__(self, index, value):
+        cdef slice index_slice
+        cdef long int start, stop
+
+        if isinstance(value, ChromVector):
+            if self.array is value.array and value.iv.start == index.start and \
+                    value.iv.end == index.stop and (index.step is None or index.step == 1):
+                return
+            else:
+                raise NotImplementedError(
+                    "Required assignment signature not yet implemented.")
+
+        if isinstance(index, int):
+            self.array[index - self.iv.start] = value
+
+        elif isinstance(index, slice):
+            index_slice = index
+            if index_slice.start is not None:
+                start = index_slice.start
+                if start < self.iv.start:
+                    raise IndexError("start too small")
+            else:
+                start = self.iv.start
+            if index_slice.stop is not None:
+                stop = index_slice.stop
+                if stop > self.iv.end:
+                    raise IndexError("stop too large")
+            else:
+                stop = self.iv.end
+            if start > stop:
+                raise IndexError("Start of interval is after its end.")
+            if start == stop:
+                raise IndexError("Cannot assign to zero-length interval.")
+            self.array[start - self.offset: stop -
+                       self.iv.start: index.step] = value
+
+        elif isinstance(index, GenomicInterval):
+            if index.chrom != self.iv.chrom:
+                raise KeyError("Chromosome name mismatch.")
+            if self.iv.strand is not strand_nostrand and \
+                    self.iv.strand is not self.index.strand:
+                raise KeyError("Strand mismatch.")
+            self.array[index.iv.start - self.iv.start,
+                       index.iv.end - self.iv.start] = value
+        else:
+            raise TypeError("Illegal index type")
+
+    def __iadd__(self, value):
+        if not self.is_vector_of_sets:
+            self.array[self.iv.start - self.offset: self.iv.end -
+                       self.offset].__iadd__(value)
+        else:
+            def addval(x):
+                y = x.copy()
+                y.add(value)
+                return y
+
+            self.apply(addval)
+        return self
+
+    def __iter__(self):
+        return self.values()
+
+    def values(self):
+        return iter(self.array[self.iv.start - self.offset: self.iv.end - self.offset])
+
+    def steps(self):
+        return _HTSeq_internal.ChromVector_steps(self)
+
+    def apply(self, fun):
+        for iv, value in self.steps():
+            self.array[iv.start - self.offset: iv.end -
+                       self.offset] = fun(value)
+
+    def __repr__(self):
+        return "<%s object, %s, %s>" % (self.__class__.__name__, str(self.iv), self._storage)
+
+    def __reduce__(self):
+        assert self.__class__ is ChromVector
+        return(_ChromVector_unpickle,
+               (self.array, self.iv, self.offset, self.is_vector_of_sets, self._storage))
+
+
+def _ChromVector_unpickle(array, iv, offset, is_vector_of_sets, _storage):
+    cv = ChromVector()
+    cv.array = array
+    cv.iv = iv
+    cv.offset = offset
+    cv.is_vector_of_sets = is_vector_of_sets
+    cv._storage = _storage
+    return cv
\ No newline at end of file
diff --git a/tiny/rna/counter/stepvector/test_stepvec.pyx b/tiny/rna/counter/stepvector/test_stepvec.pyx
new file mode 100644
index 00000000..fb7a3dcf
--- /dev/null
+++ b/tiny/rna/counter/stepvector/test_stepvec.pyx
@@ -0,0 +1,32 @@
+# distutils: language = c++
+# cython: language_level = 3
+
+from cpython.ref cimport PyObject
+from cython.operator cimport dereference as deref, preincrement as inc, address
+
+from ._stepvector cimport _StepVector, PyRef
+ctypedef PyObject* PyPtr
+
+def main():
+    cdef PyRef r1, r2, r3, c1, c2
+
+    vctre = new _StepVector[PyRef]()
+    f1 = {"featA"}
+    f2 = {"featB", "featC"}
+    f3 = {"featD"}
+    r1 = PyRef(<PyPtr>f1)
+    r2 = PyRef(<PyPtr>f2)
+    r3 = PyRef(<PyPtr>f3)
+
+    vctre.add_value(11, 99, r1)
+    vctre.add_value(22, 44, r2)
+    vctre.add_value(33, 98, r3)
+
+    it = vctre.begin()
+    while it != vctre.end():
+        step = deref(it)
+        print(f"{<int> step.first}: {<object> (<PyRef>step.second).get()}")
+        inc(it)
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file

From 68162a8780ee606e7981e16fd97e765335007361 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Mon, 22 Aug 2022 18:02:17 -0700
Subject: [PATCH 12/29] Added a basic usage Python-space unit test for the
 Cython StepVector

---
 tests/unit_tests_stepvector.py | 88 ++++++++++++++++++++++++++++++++++
 1 file changed, 88 insertions(+)
 create mode 100644 tests/unit_tests_stepvector.py

diff --git a/tests/unit_tests_stepvector.py b/tests/unit_tests_stepvector.py
new file mode 100644
index 00000000..05f03106
--- /dev/null
+++ b/tests/unit_tests_stepvector.py
@@ -0,0 +1,88 @@
+import unittest
+import HTSeq
+
+from tiny.rna.counter.stepvector._stepvector import StepVector
+
+
+class StepVectorTests(unittest.TestCase):
+
+    """Does our Cython StepVector accept and return steps as expected?"""
+
+    def test_genomicarray_with_cython_stepvec(self):
+        # Patch the StepVector reference in the HTSeq module and use a GenomicArray
+        # instead of a GenomicArrayOfSets, just as we do in ReferenceTables
+        setattr(HTSeq.StepVector, 'StepVector', StepVector)
+        gas = HTSeq.GenomicArray('auto', stranded=False)
+
+        iv1 = HTSeq.GenomicInterval("chr", 0, 5)
+        iv2 = HTSeq.GenomicInterval("chr", 5, 7)
+        iv3 = HTSeq.GenomicInterval("chr", 4, 6)
+        iv4 = HTSeq.GenomicInterval("chr", 7, 9)
+        ivs = [iv1, iv2, iv3, iv4]
+
+        f1 = {'featA'}
+        f2 = {'featB', 'featC'}
+        f3 = {'featD'}
+        f4 = {'featE', 'featF', 'featG'}
+        fs = [f1, f2, f3, f4]
+
+        """
+        iv1:  0 |-----| 5       featA
+        iv2:       5 |--| 7     featB, featC
+        iv3:      4 |--| 6      featD
+        iv4:         7 |--| 9   featE, featF, featG
+        """
+
+        for iv, feat in zip(ivs, fs):
+            gas[iv] += feat
+
+        exp_overlaps = [
+            [(0, 4, f1), (4, 5, f1 | f3)],  # f1 overlaps f3
+            [(5, 6, f2 | f3), (6, 7, f2)],  # f2 overlaps f3
+            [(4, 5, f1 | f3), (5, 6, f3 | f2)],  # f3 overlaps f1 and f2
+            [(7, 9, f4)],  # f4 does not overlap anything else
+        ]
+
+        for iv, expected in zip(ivs, exp_overlaps):
+            actual = list(gas['chr']['.'].array[iv.start:iv.end].get_steps())
+            self.assertEqual(actual, expected)
+
+    def test_compare_to_htseq_steps(self):
+        """Test currently doesn't work (and it won't be easy to get it to work)
+
+        This is because HTSeq's StepVector with typecode 'O' handles .add_value() using the
+        apply() function and a local function which copies the set OUT of the StepVector,
+        adds to it, then puts it back. This is exactly the kind of thing that our
+        specialized StepVector was intended to avoid.
+        """
+
+        from HTSeq.StepVector import StepVector as hStepVector
+        def htseq_add(x):
+            y = x.copy()
+            y.add(value)
+            return y
+
+        sv_len = 200
+        ours = StepVector.create(length=sv_len)
+        theirs = hStepVector.create(length=sv_len, typecode='O')
+        
+        iv1 = slice(0, 99)
+        iv2 = slice(99, 101)
+        iv3 = slice(98, 100)
+        iv4 = slice(101, 150)
+        ivs = [iv1, iv2, iv3, iv4]
+
+        f1 = {'featA'}
+        f2 = {'featB', 'featC'}
+        f3 = {'featD'}
+        f4 = {'featE', 'featF', 'featG'}
+        fs = [f1, f2, f3, f4]
+
+        for iv, feat in zip(ivs, fs):
+            value = feat
+            theirs[iv].apply(htseq_add)
+            ours[iv] += feat
+
+
+if __name__ == '__main__':
+    unittest.main()

From 3a8baa87e2328fbd2f74e0e392046ab5e72bf66c Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Mon, 22 Aug 2022 18:37:42 -0700
Subject: [PATCH 13/29] A slightly more efficient routine for converting values
 to lowercase in CaseInsensitiveDict

---
 tiny/rna/counter/hts_parsing.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tiny/rna/counter/hts_parsing.py b/tiny/rna/counter/hts_parsing.py
index b65cecd4..a1460fd8 100644
--- a/tiny/rna/counter/hts_parsing.py
+++ b/tiny/rna/counter/hts_parsing.py
@@ -248,7 +248,7 @@ def __init__(self):
         super().__init__()
 
     def __setitem__(self, key: str, vals: tuple):
-        lowercase_vals = tuple(v.lower() for v in vals)
+        lowercase_vals = tuple(map(str.lower, vals))
         super().__setitem__(key.lower(), (key, vals, lowercase_vals))
 
     def __getitem__(self, key: str):

From 0e79b38006f35523df19024abedbc4a120b7a11f Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sat, 24 Sep 2022 15:05:24 -0700
Subject: [PATCH 14/29] Adding beta command line arguments for tiny-count to
 CWL and Run Config

---
 tiny/cwl/tools/tiny-count.cwl     | 15 +++++++++++++++
 tiny/cwl/workflows/tinyrna_wf.cwl |  8 +++++++-
 tiny/rna/counter/counter.py       |  8 ++++++++
 tiny/rna/counter/hts_parsing.py   |  9 +++++----
 4 files changed, 35 insertions(+), 5 deletions(-)

diff --git a/tiny/cwl/tools/tiny-count.cwl b/tiny/cwl/tools/tiny-count.cwl
index c899854b..b67204c8 100644
--- a/tiny/cwl/tools/tiny-count.cwl
+++ b/tiny/cwl/tools/tiny-count.cwl
@@ -53,6 +53,21 @@ inputs:
     inputBinding:
       prefix: -dc
 
+  id_attr:
+    type: string?
+    inputBinding:
+      prefix: -id
+
+  stepvector:
+    type: string?
+    inputBinding:
+      prefix: -sv
+
+  multi_id:
+    type: boolean?
+    inputBinding:
+      prefix: -md
+
   all_features:
     type: boolean?
     inputBinding:
diff --git a/tiny/cwl/workflows/tinyrna_wf.cwl b/tiny/cwl/workflows/tinyrna_wf.cwl
index 4786878f..8aa9ab0e 100644
--- a/tiny/cwl/workflows/tinyrna_wf.cwl
+++ b/tiny/cwl/workflows/tinyrna_wf.cwl
@@ -82,10 +82,13 @@ inputs:
   aligned_seqs: File[]?
   is_pipeline: boolean?
   counter_diags: boolean?
+  counter_id_attr: string?
   counter_decollapse: boolean?
+  counter_stepvector: string?
   counter_all_features: boolean?
   counter_type_filter: string[]?
   counter_source_filter: string[]?
+  counter_allow_multi_id: boolean?
   counter_normalize_by_hits: boolean?
 
   # deseq inputs
@@ -208,11 +211,14 @@ steps:
       out_prefix: run_name
       all_features: counter_all_features
       source_filter: counter_source_filter
+      type_filter: counter_type_filter
       normalize_by_hits:
         source: counter_normalize_by_hits
         valueFrom: $(String(self))  # convert boolean -> string
       decollapse: counter_decollapse
-      type_filter: counter_type_filter
+      id_attr: counter_id_attr
+      multi_id: counter_allow_multi_id
+      stepvector: counter_stepvector
       is_pipeline: {default: true}
       diagnostics: counter_diags
       fastp_logs: preprocessing/json_report_file
diff --git a/tiny/rna/counter/counter.py b/tiny/rna/counter/counter.py
index f84fe926..c6979086 100644
--- a/tiny/rna/counter/counter.py
+++ b/tiny/rna/counter/counter.py
@@ -60,8 +60,16 @@ def get_args():
     optional_args.add_argument('-d', '--report-diags', action='store_true',
                                help='Produce diagnostic information about uncounted/eliminated '
                                     'selection elements.')
+
+    # Beta arguments
     optional_args.add_argument('-sv', '--step-vector', choices=['Cython', 'HTSeq'], default='Cython',
                                help='Select which StepVector is used for interval -> feature resolution.')
+    optional_args.add_argument('-id', '--id-attr', metavar='KEY', default="id",
+                               help="Set the column 9 attribute key that should serve as the ID "
+                                    "attribute. This is usually 'id' or 'gene_id'.")
+    optional_args.add_argument('-md', '--multi-id', action='store_true',
+                               help="Don't treat features with multiple ID values as an error. "
+                                    "Only the first value will be used as the feature's ID.")
 
     args = arg_parser.parse_args()
     setattr(args, 'normalize_by_hits', args.normalize_by_hits.lower() in ['t', 'true'])
diff --git a/tiny/rna/counter/hts_parsing.py b/tiny/rna/counter/hts_parsing.py
index a1460fd8..c730c177 100644
--- a/tiny/rna/counter/hts_parsing.py
+++ b/tiny/rna/counter/hts_parsing.py
@@ -362,6 +362,8 @@ class ReferenceTables:
 
     def __init__(self, gff_files: Dict[str, list], feature_selector, **prefs):
         self.all_features = prefs.get('all_features', False)
+        self.multi_id = prefs.get('multi_id', False)
+        self.id_attr = prefs.get('id_attr', 'ID')
         self.selector = feature_selector
         self._set_filters(**prefs)
         self.gff_files = gff_files
@@ -614,15 +616,14 @@ def chrom_vector_setdefault(self, chrom):
         if chrom not in self.feats.chrom_vectors:
             self.feats.add_chrom(chrom)
 
-    @staticmethod
-    def get_feature_id(row):
-        id_collection = row.attr.get("ID", None)
+    def get_feature_id(self, row):
+        id_collection = row.attr.get(self.id_attr, None)
 
         if id_collection is None:
             raise ValueError(f"Feature {row.name} does not contain an ID attribute.")
         if len(id_collection) == 0:
             raise ValueError("A feature's ID attribute cannot be empty. This value is required.")
-        if len(id_collection) > 1:
+        if len(id_collection) > 1 and not self.multi_id:
             err_msg = "A feature's ID attribute cannot contain multiple values. Only one ID per feature is allowed."
             raise ValueError(err_msg)
 

From acc23bee6bc56eebeac922f35d6d64f555c03754 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 28 Sep 2022 17:01:10 -0700
Subject: [PATCH 15/29] Adding a basic native C++ test for the wrapped core of
 the Cython StepVector

---
 tests/cython_tests/stepvector/Makefile      | 15 ++++++
 tests/cython_tests/stepvector/test_core.cpp | 51 +++++++++++++++++++++
 2 files changed, 66 insertions(+)
 create mode 100755 tests/cython_tests/stepvector/Makefile
 create mode 100644 tests/cython_tests/stepvector/test_core.cpp

diff --git a/tests/cython_tests/stepvector/Makefile b/tests/cython_tests/stepvector/Makefile
new file mode 100755
index 00000000..35b0756d
--- /dev/null
+++ b/tests/cython_tests/stepvector/Makefile
@@ -0,0 +1,15 @@
+CXX        := clang++
+
+PY_VERS    := python3.9
+PY_CFLAGS  := $(shell ${PY_VERS}-config --cflags --libs)
+PY_LDFLAGS := $(shell ${PY_VERS}-config --ldflags --embed)
+
+INCLUDE    := -I$(realpath ../../../tiny/rna/counter/stepvector/src)
+LDFLAGS    := ${PY_LDFLAGS} -L${CONDA_PREFIX}/lib -rpath ${CONDA_PREFIX}/lib
+CXXFLAGS   := -std=c++17 -stdlib=libc++ ${INCLUDE} ${PY_CFLAGS}
+
+test_core : test_core.cpp
+	$(CXX) $(CXXFLAGS) $(LDFLAGS) $^ -o $@
+
+clean :
+	@rm -f test_core
\ No newline at end of file
diff --git a/tests/cython_tests/stepvector/test_core.cpp b/tests/cython_tests/stepvector/test_core.cpp
new file mode 100644
index 00000000..895f8f35
--- /dev/null
+++ b/tests/cython_tests/stepvector/test_core.cpp
@@ -0,0 +1,51 @@
+#include "StepVector.h"
+#include "PyRef.h"
+
+using sparse_vectors::_StepVector;
+using PyPtr::PyRef;
+
+int main(){
+    Py_Initialize();
+
+    _StepVector<PyRef> sv;
+
+    PyObject *c1 = PySet_New(NULL); // {featA, featB}
+    PyObject *c2 = PySet_New(NULL); // {featC}
+    PyObject *c3 = PySet_New(NULL); // {featD}
+
+    PyObject *sA = PyUnicode_FromString("featA");
+    PyObject *sB = PyUnicode_FromString("featB");
+    PyObject *sC = PyUnicode_FromString("featC");
+    PyObject *sD = PyUnicode_FromString("featD");
+
+    PySet_Add(c1, sA);
+    PySet_Add(c1, sB);
+    PySet_Add(c2, sC);
+    PySet_Add(c3, sD);
+
+    PyRef p1 = PyRef(c1);
+    PyRef p2 = PyRef(c2);
+    PyRef p3 = PyRef(c3);
+
+    sv.add_value(0, 10, p1);
+    sv.add_value(8, 15, p2);
+    sv.add_value(9, 20, p3);
+
+    std::cout << std::endl;
+
+    for (auto it = sv.get_values(-1); it != sv.end(); ++it){
+        std::cout << it->first << ": ";
+        PyObject_Print(it->second.get(), stdout, 0);
+        std::cout << std::endl;
+    }
+
+    /* Expect:
+    -9223372036854775808: set()
+    0: {'featA', 'featB'}
+    8: {'featA', 'featC', 'featB'}
+    9: {'featD', 'featA', 'featC', 'featB'}
+    11: {'featD', 'featC'}
+    16: {'featD'}
+    21: set()
+    */
+}
\ No newline at end of file

From faeeeb0e64a15b9f0c9abdd7e22f140846756ecd Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 28 Sep 2022 17:02:04 -0700
Subject: [PATCH 16/29] Adding a basic Cython test for the StepVector

---
 tests/cython_tests/__init__.py                |  0
 tests/cython_tests/stepvector/__init__.py     |  0
 tests/cython_tests/stepvector/test_cython.pyx | 54 +++++++++++++++++++
 tiny/rna/counter/stepvector/test_stepvec.pyx  | 32 -----------
 4 files changed, 54 insertions(+), 32 deletions(-)
 create mode 100644 tests/cython_tests/__init__.py
 create mode 100644 tests/cython_tests/stepvector/__init__.py
 create mode 100644 tests/cython_tests/stepvector/test_cython.pyx
 delete mode 100644 tiny/rna/counter/stepvector/test_stepvec.pyx

diff --git a/tests/cython_tests/__init__.py b/tests/cython_tests/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/cython_tests/stepvector/__init__.py b/tests/cython_tests/stepvector/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/tests/cython_tests/stepvector/test_cython.pyx b/tests/cython_tests/stepvector/test_cython.pyx
new file mode 100644
index 00000000..7a7e15c9
--- /dev/null
+++ b/tests/cython_tests/stepvector/test_cython.pyx
@@ -0,0 +1,54 @@
+# distutils: language = c++
+# cython: language_level = 3
+import sys
+
+from cpython.ref cimport PyObject
+from libcpp.pair cimport pair
+from cython.operator cimport dereference as deref, preincrement as inc, postincrement as pinc
+
+from tiny.rna.counter.stepvector._stepvector cimport _StepVector, PyRef
+ctypedef PyObject* PyPtr
+
+def main():
+    cdef PyRef p1, p2, p3
+
+    sv = new _StepVector[PyRef]()
+
+    c1 = {"featA", "featB"}
+    c2 = {"featC"}
+    c3 = {"featD"}
+    p1 = PyRef(<PyPtr>c1)
+    p2 = PyRef(<PyPtr>c2)
+    p3 = PyRef(<PyPtr>c3)
+
+    sv.add_value(0, 10, p1)
+    sv.add_value(8, 15, p2)
+    sv.add_value(9, 20, p3)
+
+    it = sv.get_values(-1)
+    expected = iter([
+        ((-1 * sys.maxsize - 1), set()),
+        (0, {'featA', 'featB'}),
+        (8, {'featA', 'featB', 'featC'}),
+        (9, {'featA', 'featB', 'featC', 'featD'}),
+        (11, {'featC', 'featD'}),
+        (16, {'featD'}),
+        (21, set())
+    ])
+
+    while it != sv.end():
+        step = deref(pinc(it))
+        exp_pos, exp_set = next(expected)
+
+        try:
+            assert step.first == exp_pos
+            assert <object>step.second.get() == exp_set
+        except AssertionError as e:
+            print(f"Expected {exp_pos}: {exp_set}")
+            print(f"Received {step.first}: {<object>step.second.get()}")
+            raise
+
+    print("StepVector basic test passed.")
+
+if __name__ == '__main__':
+    main()
\ No newline at end of file
diff --git a/tiny/rna/counter/stepvector/test_stepvec.pyx b/tiny/rna/counter/stepvector/test_stepvec.pyx
deleted file mode 100644
index fb7a3dcf..00000000
--- a/tiny/rna/counter/stepvector/test_stepvec.pyx
+++ /dev/null
@@ -1,32 +0,0 @@
-# distutils: language = c++
-# cython: language_level = 3
-
-from cpython.ref cimport PyObject
-from cython.operator cimport dereference as deref, preincrement as inc, address
-
-from ._stepvector cimport _StepVector, PyRef
-ctypedef PyObject* PyPtr
-
-def main():
-    cdef PyRef r1, r2, r3, c1, c2
-
-    vctre = new _StepVector[PyRef]()
-    f1 = {"featA"}
-    f2 = {"featB", "featC"}
-    f3 = {"featD"}
-    r1 = PyRef(<PyPtr>f1)
-    r2 = PyRef(<PyPtr>f2)
-    r3 = PyRef(<PyPtr>f3)
-
-    vctre.add_value(11, 99, r1)
-    vctre.add_value(22, 44, r2)
-    vctre.add_value(33, 98, r3)
-
-    it = vctre.begin()
-    while it != vctre.end():
-        step = deref(it)
-        print(f"{<int> step.first}: {<object> (<PyRef>step.second).get()}")
-        inc(it)
-
-if __name__ == '__main__':
-    main()
\ No newline at end of file

From c31f82f29d7f18a70437548c23551549b0407f12 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 28 Sep 2022 17:04:52 -0700
Subject: [PATCH 17/29] Improved Cython-related code in setup.py so that
 macOS-specific compile args aren't used on other platforms. Also cleaning up
 some boilerplate code

---
 setup.py | 28 ++++++++++++++--------------
 1 file changed, 14 insertions(+), 14 deletions(-)

diff --git a/setup.py b/setup.py
index 6652ec49..d23fdb43 100644
--- a/setup.py
+++ b/setup.py
@@ -29,26 +29,26 @@ def run(self):
     def in_conda_env(self):
         return all([os.getenv(conda_var) for conda_var in ["CONDA_PREFIX", "CONDA_DEFAULT_ENV"]])
 
-debug_cython = False
+
+pyx_files = [
+    'tiny/rna/counter/stepvector/_stepvector.pyx',
+    'tests/cython_tests/stepvector/test_cython.pyx'
+]
 cxx_extension_args = {
-    'extra_compile_args': [
-        '-isystem', '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include',
-        '-stdlib=libc++', '-std=c++11',
-        '-O3'],
-    'extra_link_args': ['-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib'],
+    'extra_compile_args': ['-stdlib=libc++', '-std=c++11', '-O3'],
+    'extra_link_args': [],
     'language': 'c++'
 }
+if sys.platform == "darwin":
+    cxx_extension_args['extra_compile_args'] += ['-isystem', '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include']
+    cxx_extension_args['extra_link_args'] += ['-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib']
 cython_extensions = [
     setuptools.Extension(
-        "tiny.rna.counter.stepvector._stepvector",
-        sources=['tiny/rna/counter/stepvector/_stepvector.pyx'],
-        **cxx_extension_args
-    ),
-    setuptools.Extension(
-        "tiny.rna.counter.stepvector.test_stepvec",
-        sources=['tiny/rna/counter/stepvector/test_stepvec.pyx'],
+        pyx_filename.replace('/', '.').rstrip('.pyx'),
+        sources=[pyx_filename],
         **cxx_extension_args
     )
+    for pyx_filename in pyx_files
 ]
 
 setuptools.setup(
@@ -73,7 +73,7 @@ def in_conda_env(self):
     ext_modules=cythonize(
         cython_extensions,
         compiler_directives={'language_level': '3'},
-        gdb_debug=debug_cython
+        gdb_debug=False
     ),
     scripts=['tiny/rna/tiny-deseq.r'],
     classifiers=[

From 9deede8916fdf8da7c69cdf61b693565a8ccc948 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 28 Sep 2022 17:07:57 -0700
Subject: [PATCH 18/29] Debug statements in PyRef have been changed to
 preprocessor directives. This has the advantage of 1) skipping the condition
 checks if not built with debugging enabled, and 2) the debug member variable
 in the PyRef class was bad design, and this allows it to be removed.

---
 tiny/rna/counter/stepvector/src/PyRef.h | 45 ++++++++++++++++---------
 1 file changed, 29 insertions(+), 16 deletions(-)

diff --git a/tiny/rna/counter/stepvector/src/PyRef.h b/tiny/rna/counter/stepvector/src/PyRef.h
index 3458d649..8a89190c 100644
--- a/tiny/rna/counter/stepvector/src/PyRef.h
+++ b/tiny/rna/counter/stepvector/src/PyRef.h
@@ -2,13 +2,21 @@
 #include <iostream>
 #include <cstring>
 
+//#define DEBUG
+
 namespace PyPtr {
     class PyRef {
         PyObject* obj;
-        bool debug = false;
 
         public:
-            PyObject* get() const {return obj;}
+            PyObject* get() const {
+                #ifdef DEBUG
+                    std::cout << "Retrieve: ";
+                    PyObject_Print(obj, stdout, 0);
+                    std::cout << " (obj: " << obj << ")" << std::endl;
+                #endif
+                return obj;
+            }
 
             // Default constructor
             PyRef() {
@@ -28,15 +36,20 @@ namespace PyPtr {
                     PySet_Add(obj, payload);
                 }
 
-                if (debug){
+                #ifdef DEBUG
                     std::cout << "Object ctor: ";
                     PyObject_Print(payload, stdout, 0);
                     std::cout << " (obj: " << obj << ")" << std::endl;
-                }
+                #endif
             }
 
             // Destructor
             ~PyRef() {
+                #ifdef DEBUG
+                    std::cout << "Object destructor: ";
+                    PyObject_Print(obj, stdout, 0);
+                    std::cout << " (obj: " << obj << ")" << std::endl;
+                #endif
                 Py_XDECREF(obj);
             }
 
@@ -44,22 +57,22 @@ namespace PyPtr {
             PyRef(const PyRef& other) {
                 obj = PySet_New(other.obj);
 
-                if (debug) {
+                #ifdef DEBUG
                     std::cout << "Copy ctor: ";
                     PyObject_Print(other.obj, stdout, 0);
                     std::cout << " (obj: " << other.obj << " -> " << obj << ")";
                     std::cout << std::endl << std::flush;
-                }
+                #endif
             }
 
             // Move constructor
             PyRef(PyRef&& other) {
-                if (debug) {
+                #ifdef DEBUG
                     std::cout << "Move ctor: ";
                     PyObject_Print(other.obj, stdout, 0);
                     std::cout << " (obj: " << other.obj << ")";
                     std::cout << std::endl << std::flush;
-                }
+                #endif
 
                 obj = other.obj;
                 Py_XDECREF(other.obj);
@@ -67,12 +80,12 @@ namespace PyPtr {
 
             // Assignment
             PyRef& operator=(const PyRef& other) {
-                if (debug) {
+                #ifdef DEBUG
                     std::cout << "Assignment: ";
                     PyObject_Print(other.obj, stdout, 0);
                     std::cout << " (obj: " << other.obj << ")";
                     std::cout << std::endl << std::flush;
-                }
+                #endif
 
                 Py_XDECREF(obj);
                 obj = PySet_New(other.obj);
@@ -81,12 +94,12 @@ namespace PyPtr {
 
             // Move assignment
             PyRef& operator=(PyRef&& other) {
-                if (debug) {
+                #ifdef DEBUG
                     std::cout << "Move assignment: ";
                     PyObject_Print(other.obj, stdout, 0);
                     std::cout << " (obj: " << other.obj << ")";
                     std::cout << std::endl << std::flush;
-                }
+                #endif
 
                 Py_XDECREF(obj);
                 obj = other.obj;
@@ -96,9 +109,9 @@ namespace PyPtr {
             }
 
             PyRef& operator+= (const PyRef& other) {
-                if (debug) {
+                #ifdef DEBUG
                     std::cout << "+=" << std::endl;
-                }
+                #endif
 
                 if (PySet_Check(other.obj)){
                     _PySet_Update(obj, PyObject_GetIter(other.obj));
@@ -109,12 +122,12 @@ namespace PyPtr {
             }
 
             PyRef operator+ (const PyRef& rhs) {
-                if (debug){
+                #ifdef DEBUG
                     PyObject_Print(obj, stdout, 0);
                     std::cout << " + ";
                     PyObject_Print(rhs.obj, stdout, 0);
                     std::cout << std::endl;
-                }
+                #endif
 
                 PyRef result(obj);
                 if (PySet_Check(rhs.obj)){

From 20086b2bdcba5ba5d4ed433ff6c097c1b55b21e8 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 28 Sep 2022 17:08:32 -0700
Subject: [PATCH 19/29] Small performance improvements

---
 tiny/rna/counter/features.py    | 15 ++++++---------
 tiny/rna/counter/hts_parsing.py |  7 ++-----
 2 files changed, 8 insertions(+), 14 deletions(-)

diff --git a/tiny/rna/counter/features.py b/tiny/rna/counter/features.py
index a322587e..22bb7038 100644
--- a/tiny/rna/counter/features.py
+++ b/tiny/rna/counter/features.py
@@ -40,20 +40,17 @@ def __init__(self, gff_file_set, selection_rules, **prefs):
     def assign_features(self, al: dict) -> Tuple[dict, int]:
         """Determines features associated with the interval then performs rule-based feature selection"""
 
-        feat_matches, assignment = set(), {}
-
         try:
-            feat_matches = feat_matches.union(*(
-                    Features.chrom_vectors[al['Chrom']]['.']  # GenomicArrayOfSets -> ChromVector
-                             .array[al['Start']:al['End']]    # ChromVector -> StepVector
-                             .get_steps(values_only=True)))   # StepVector -> {features}
+            feat_matches = set().union(
+                            *Features.chrom_vectors[al['Chrom']]['.']  # GenomicArrayOfSets -> ChromVector
+                                     .array[al['Start']:al['End']]     # ChromVector -> StepVector
+                                     .get_steps(values_only=True))     # StepVector -> {features}
         except KeyError as ke:
             self.stats.chrom_misses[ke.args[0]] += 1
+            return {}, 0
 
         # If features are associated with the alignment interval, perform selection
-        if len(feat_matches):
-            assignment = self.selector.choose(feat_matches, al)
-
+        assignment = self.selector.choose(feat_matches, al) if feat_matches else {}
         return assignment, len(feat_matches)
 
     def count_reads(self, library: dict):
diff --git a/tiny/rna/counter/hts_parsing.py b/tiny/rna/counter/hts_parsing.py
index d938cc03..c974d816 100644
--- a/tiny/rna/counter/hts_parsing.py
+++ b/tiny/rna/counter/hts_parsing.py
@@ -268,18 +268,15 @@ def parse_GFF_attribute_string(attrStr, extra_return_first_value=False, gff_vers
         ID."
     """
 
-    if attrStr.endswith("\n"):
-        attrStr = attrStr[:-1]
-
     # Modification: store attributes in a dict subclass that allows case-insensitive ops
     attribute_dict = CaseInsensitiveAttrs()
     first_val = "_unnamed_"
 
     if gff_version == 2:
-        iterator = HTSeq._HTSeq.quotesafe_split(attrStr.encode())
+        iterator = HTSeq._HTSeq.quotesafe_split(attrStr.rstrip().encode())
     else:
         # GFF3 does not care about quotes
-        iterator = attrStr.encode().split(b';')
+        iterator = attrStr.rstrip().encode().split(b';')
 
     for i, attr in enumerate(iterator):
         attr = attr.decode()

From db3df05a3df172b9ba78e722514536ecedb07d81 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 28 Sep 2022 17:28:00 -0700
Subject: [PATCH 20/29] Adding a very basic check to make sure that the Cython
 StepVector has been built on the user's machine. If not, tiny-count produces
 an error and exists. This should only be relevant if the user is running
 tinyRNA from the project directory, so the error message has been written
 accordingly

---
 tiny/rna/counter/hts_parsing.py | 12 +++++++++---
 1 file changed, 9 insertions(+), 3 deletions(-)

diff --git a/tiny/rna/counter/hts_parsing.py b/tiny/rna/counter/hts_parsing.py
index c974d816..631f39aa 100644
--- a/tiny/rna/counter/hts_parsing.py
+++ b/tiny/rna/counter/hts_parsing.py
@@ -448,9 +448,15 @@ def __init__(self, gff_files: Dict[str, list], feature_selector, **prefs):
         self.gff_files = gff_files
         # ----------------------------------------------------------- Primary Key:
         if prefs['step_vector'] == 'Cython':
-            from tiny.rna.counter.stepvector import StepVector
-            setattr(HTSeq.StepVector, 'StepVector', StepVector)
-            self.feats = HTSeq.GenomicArray("auto", stranded=False)         # Root Match ID
+            try:
+                from tiny.rna.counter.stepvector import StepVector
+                setattr(HTSeq.StepVector, 'StepVector', StepVector)
+                self.feats = HTSeq.GenomicArray("auto", stranded=False)     # Root Match ID
+            except ModuleNotFoundError:
+                print("The Cython StepVector has not yet been built.\n"
+                      "Run: python setup.py build_ext --inplace",
+                      file=sys.stderr)
+                sys.exit(1)
         else:
             self.feats = HTSeq.GenomicArrayOfSets("auto", stranded=False)   # Root Match ID
 

From 737a33335e7c7b2ecb3a6f6f5510521edf074c93 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 28 Sep 2022 18:05:30 -0700
Subject: [PATCH 21/29] Removing the id_attr beta option from tiny-count. Since
 multiple annotation files can be used for counting and they may be
 heterogenous in type, this option will need to be defined for each file if we
 decide to include it.

ReferenceTables has been changed to also use "gene_id" as a feature's ID attribute. "ID" is still considered the primary attribute if both are present. This should make things easier for users with GFF2/GTF files
---
 START_HERE/run_config.yml              | 7 +++++++
 tiny/cwl/tools/tiny-count.cwl          | 5 -----
 tiny/cwl/workflows/tinyrna_wf.cwl      | 2 --
 tiny/rna/counter/counter.py            | 3 ---
 tiny/rna/counter/hts_parsing.py        | 7 +++----
 tiny/templates/run_config_template.yml | 7 +++++++
 6 files changed, 17 insertions(+), 14 deletions(-)

diff --git a/START_HERE/run_config.yml b/START_HERE/run_config.yml
index ea9d4aa3..9de0e9cc 100644
--- a/START_HERE/run_config.yml
+++ b/START_HERE/run_config.yml
@@ -244,6 +244,13 @@ counter_source_filter: []
 ##-- If source AND type filters are given, a line must match both to be included --##
 counter_type_filter: []
 
+##-- Select the StepVector implementation that is used. Options: HTSeq or Cython --##
+counter_stepvector: 'Cython'
+
+##-- If False: a feature with multiple values in its ID attribute is treated as an error --##
+##-- If True: multiple ID values are allowed, but only the first value is used --##
+counter_allow_multi_id: True
+
 ##-- If True: produce diagnostic logs to indicate what was eliminated and why --##
 counter_diags: False
 
diff --git a/tiny/cwl/tools/tiny-count.cwl b/tiny/cwl/tools/tiny-count.cwl
index 273275d4..cfaf77b4 100644
--- a/tiny/cwl/tools/tiny-count.cwl
+++ b/tiny/cwl/tools/tiny-count.cwl
@@ -53,11 +53,6 @@ inputs:
     inputBinding:
       prefix: -dc
 
-  id_attr:
-    type: string?
-    inputBinding:
-      prefix: -id
-
   stepvector:
     type: string?
     inputBinding:
diff --git a/tiny/cwl/workflows/tinyrna_wf.cwl b/tiny/cwl/workflows/tinyrna_wf.cwl
index abc9fe4b..ccd59926 100644
--- a/tiny/cwl/workflows/tinyrna_wf.cwl
+++ b/tiny/cwl/workflows/tinyrna_wf.cwl
@@ -82,7 +82,6 @@ inputs:
   aligned_seqs: File[]?
   is_pipeline: boolean?
   counter_diags: boolean?
-  counter_id_attr: string?
   counter_decollapse: boolean?
   counter_stepvector: string?
   counter_all_features: boolean?
@@ -216,7 +215,6 @@ steps:
         source: counter_normalize_by_hits
         valueFrom: $(String(self))  # convert boolean -> string
       decollapse: counter_decollapse
-      id_attr: counter_id_attr
       multi_id: counter_allow_multi_id
       stepvector: counter_stepvector
       is_pipeline: {default: true}
diff --git a/tiny/rna/counter/counter.py b/tiny/rna/counter/counter.py
index e6c6a733..195d3ce5 100644
--- a/tiny/rna/counter/counter.py
+++ b/tiny/rna/counter/counter.py
@@ -64,9 +64,6 @@ def get_args():
     # Beta arguments
     optional_args.add_argument('-sv', '--step-vector', choices=['Cython', 'HTSeq'], default='Cython',
                                help='Select which StepVector is used for interval -> feature resolution.')
-    optional_args.add_argument('-id', '--id-attr', metavar='KEY', default="id",
-                               help="Set the column 9 attribute key that should serve as the ID "
-                                    "attribute. This is usually 'id' or 'gene_id'.")
     optional_args.add_argument('-md', '--multi-id', action='store_true',
                                help="Don't treat features with multiple ID values as an error. "
                                     "Only the first value will be used as the feature's ID.")
diff --git a/tiny/rna/counter/hts_parsing.py b/tiny/rna/counter/hts_parsing.py
index 631f39aa..533983bf 100644
--- a/tiny/rna/counter/hts_parsing.py
+++ b/tiny/rna/counter/hts_parsing.py
@@ -441,8 +441,7 @@ class ReferenceTables:
 
     def __init__(self, gff_files: Dict[str, list], feature_selector, **prefs):
         self.all_features = prefs.get('all_features', False)
-        self.multi_id = prefs.get('multi_id', False)
-        self.id_attr = prefs.get('id_attr', 'ID')
+        self.allow_multi_id = prefs.get('multi_id', False)
         self.selector = feature_selector
         self._set_filters(**prefs)
         self.gff_files = gff_files
@@ -702,13 +701,13 @@ def chrom_vector_setdefault(self, chrom):
             self.feats.add_chrom(chrom)
 
     def get_feature_id(self, row):
-        id_collection = row.attr.get(self.id_attr, None)
+        id_collection = row.attr.get('ID', row.attr.get('gene_id', None))
 
         if id_collection is None:
             raise ValueError(f"Feature {row.name} does not contain an ID attribute.")
         if len(id_collection) == 0:
             raise ValueError("A feature's ID attribute cannot be empty. This value is required.")
-        if len(id_collection) > 1 and not self.multi_id:
+        if len(id_collection) > 1 and not self.allow_multi_id:
             err_msg = "A feature's ID attribute cannot contain multiple values. Only one ID per feature is allowed."
             raise ValueError(err_msg)
 
diff --git a/tiny/templates/run_config_template.yml b/tiny/templates/run_config_template.yml
index a1ec8610..fd6f1817 100644
--- a/tiny/templates/run_config_template.yml
+++ b/tiny/templates/run_config_template.yml
@@ -244,6 +244,13 @@ counter_source_filter: []
 ##-- If source AND type filters are given, a line must match both to be included --##
 counter_type_filter: []
 
+##-- Select the StepVector implementation that is used. Options: HTSeq or Cython --##
+counter_stepvector: 'Cython'
+
+##-- If False: a feature with multiple values in its ID attribute is treated as an error --##
+##-- If True: multiple ID values are allowed, but only the first value is used --##
+counter_allow_multi_id: True
+
 ##-- If True: produce diagnostic logs to indicate what was eliminated and why --##
 counter_diags: False
 

From ae88eb6823b3b7c6c6f03fc25fd7891ac105a2db Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Wed, 28 Sep 2022 19:03:15 -0700
Subject: [PATCH 22/29] Excluding the tests directory from installation since
 the compiled Cython under tests/cython_tests/stepvector would otherwise cause
 it to be included.

---
 MANIFEST.in | 1 +
 1 file changed, 1 insertion(+)

diff --git a/MANIFEST.in b/MANIFEST.in
index fc4c9ca0..906f1d82 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -1,4 +1,5 @@
 include README.md
+exclude tests
 graft tiny
 prune **/__pycache__
 prune **/*_Outputs

From 3d2a851a8fce4545f74935c9e5aa9d86c417d93a Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sat, 1 Oct 2022 16:03:00 -0700
Subject: [PATCH 23/29] Polished the new command line argument helpstrings and
 updated documentation

---
 doc/Parameters.md           | 28 ++++++++++++++++++++++++----
 tiny/rna/counter/counter.py | 13 ++++++-------
 2 files changed, 30 insertions(+), 11 deletions(-)

diff --git a/doc/Parameters.md b/doc/Parameters.md
index aec57919..d870c454 100644
--- a/doc/Parameters.md
+++ b/doc/Parameters.md
@@ -63,14 +63,14 @@ Optional arguments:
 
 ## tiny-count
 
-### All-Features
+### All Features
 | Run Config Key         | Commandline Argument   |
 |------------------------|------------------------|
 | counter_all_features:  | `--all-features`       |
 
 By default, tiny-count will only evaluate alignments to features which match a `Select for...` & `with value...` of at least one rule in your Features Sheet. It is this matching feature set, and only this set, which is included in `feature_counts.csv` and therefore available for analysis by tiny-deseq.r and tiny-plot. Switching this option "on" will include all features in every input GFF file, regardless of attribute matches, for tiny-count and downstream steps.
 
-### Normalize-by-Hits
+### Normalize by Hits
  | Run Config Key             | Commandline Argument      |
 |----------------------------|---------------------------|
 | counter-normalize-by-hits: | `--normalize-by-hits T/F` |
@@ -92,6 +92,20 @@ The SAM files produced by the tinyRNA pipeline are collapsed by default; alignme
 
 You can optionally filter features in your GFF files by specifying sources and/or types that are desired. Source and type refer to GFF columns 2 and 3 respectively. If source _and_ type filters are specified, each feature must match one of the sources _and_ one of the types in order to be included in the counting process. For both filters, an empty list is the same as "allow all."
 
+### StepVector
+ | Run Config Key     | Commandline Argument |
+|--------------------|----------------------|
+| counter_stepvector | `--step-vector`      |
+
+A custom Cython implementation of HTSeq's StepVector is used for finding features that overlap each alignment interval. While the core C++ component of the StepVector is the same, we have found that our Cython implementation can result in runtimes up to 50% faster than HTSeq's implementation. This parameter allows you to use HTSeq's StepVector if you wish (for example, if the Cython StepVector is incompatible with your system)
+
+### Allow Features with Multiple ID Values
+ | Run Config Key         | Commandline Argument |
+|------------------------|----------------------|
+| counter_allow_multi_id | `--multi-id`         |
+
+By default, an error will be produced if a GFF file contains a feature with multiple comma separated values listed under its ID attribute. Switching this option "on" instructs tiny-count to accept these features without error, but only the first listed value is used as the ID.
+
 ### Is Pipeline
  | Run Config Key | Commandline Argument |
 |----------------|----------------------|
@@ -127,10 +141,10 @@ Required arguments:
 
 Optional arguments:
   -h, --help            show this help message and exit
-  -sf [SOURCE [SOURCE ...]], --source-filter [SOURCE [SOURCE ...]]
+  -sf [SOURCE ...], --source-filter [SOURCE ...]
                         Only produce counts for features whose GFF column 2
                         matches the source(s) listed
-  -tf [TYPE [TYPE ...]], --type-filter [TYPE [TYPE ...]]
+  -tf [TYPE ...], --type-filter [TYPE ...]
                         Only produce counts for features whose GFF column 3
                         matches the type(s) listed
   -nh T/F, --normalize-by-hits T/F
@@ -139,6 +153,12 @@ Optional arguments:
   -dc, --decollapse     Create a decollapsed copy of all SAM files listed in
                         your Samples Sheet. This option is ignored for non-
                         collapsed inputs.
+  -sv {Cython,HTSeq}, --step-vector {Cython,HTSeq}
+                        Select which StepVector implementation is used to find
+                        features overlapping an interval.
+  -md, --multi-id       Don't treat features with multiple ID values as an
+                        error. Only the first value will be used as the
+                        feature's ID.
   -a, --all-features    Represent all features in output counts table, even if
                         they did not match a Select for / with value.
   -p, --is-pipeline     Indicates that tiny-count was invoked as part of a
diff --git a/tiny/rna/counter/counter.py b/tiny/rna/counter/counter.py
index 195d3ce5..37329760 100644
--- a/tiny/rna/counter/counter.py
+++ b/tiny/rna/counter/counter.py
@@ -51,6 +51,12 @@ def get_args():
     optional_args.add_argument('-dc', '--decollapse', action='store_true',
                                help='Create a decollapsed copy of all SAM files listed in your '
                                     'Samples Sheet. This option is ignored for non-collapsed inputs.')
+    optional_args.add_argument('-sv', '--step-vector', choices=['Cython', 'HTSeq'], default='Cython',
+                               help='Select which StepVector implementation is used to find '
+                                    'features overlapping an interval.')
+    optional_args.add_argument('-md', '--multi-id', action='store_true',
+                               help="Don't treat features with multiple ID values as an error. "
+                                    "Only the first value will be used as the feature's ID.")
     optional_args.add_argument('-a', '--all-features', action='store_true',
                                help='Represent all features in output counts table, '
                                     'even if they did not match a Select for / with value.')
@@ -61,13 +67,6 @@ def get_args():
                                help='Produce diagnostic information about uncounted/eliminated '
                                     'selection elements.')
 
-    # Beta arguments
-    optional_args.add_argument('-sv', '--step-vector', choices=['Cython', 'HTSeq'], default='Cython',
-                               help='Select which StepVector is used for interval -> feature resolution.')
-    optional_args.add_argument('-md', '--multi-id', action='store_true',
-                               help="Don't treat features with multiple ID values as an error. "
-                                    "Only the first value will be used as the feature's ID.")
-
     args = arg_parser.parse_args()
     setattr(args, 'normalize_by_hits', args.normalize_by_hits.lower() in ['t', 'true'])
 

From d77f910a2a971e11a0674e886177cd5ea9ee19a5 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sat, 1 Oct 2022 16:17:37 -0700
Subject: [PATCH 24/29] Updated environment.yml to include Cython, and updated
 the lockfiles from its contents. Since subdependencies aren't version locked,
 these changes include many, many updates that have nothing to do with Cython.
 Testing shows expected outputs on macOS and Linux using these lockfiles.
 Unfortunately I don't have a better solution for this at the moment.

---
 conda/conda-linux-64.lock | 242 +++++++++++++++++++-------------------
 conda/conda-osx-64.lock   | 225 ++++++++++++++++++-----------------
 conda/environment.yml     |   1 +
 3 files changed, 233 insertions(+), 235 deletions(-)

diff --git a/conda/conda-linux-64.lock b/conda/conda-linux-64.lock
index df6acb44..88ba3f65 100644
--- a/conda/conda-linux-64.lock
+++ b/conda/conda-linux-64.lock
@@ -1,23 +1,22 @@
 # Generated by conda-lock.
 # platform: linux-64
-# input_hash: d9433cf548826db3a4d918dce3ebcfa5793ad683ff22014c94c1796381c86f17
+# input_hash: ef26dba2670179c6605442a613aa0567cc43b352efe64eaefbb5399ddc41e110
 @EXPLICIT
 https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2#d7c89558ba9fa0495403155b64376d81
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-https://conda.anaconda.org/main/linux-64/ca-certificates-2022.07.19-h06a4308_0.tar.bz2#ef4b29ea120fdfa542adbce43d035c95
+https://conda.anaconda.org/conda-forge/linux-64/ca-certificates-2022.9.24-ha878542_0.tar.bz2#41e4e87062433e283696cf384f952ef6
 https://conda.anaconda.org/main/noarch/font-ttf-dejavu-sans-mono-2.37-hd3eb1b0_0.tar.bz2#801b4743a301a4e11cbd9609d418e101
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 https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.36.1-hea4e1c9_2.tar.bz2#bd4f2e711b39af170e7ff15163fe87ee
-https://conda.anaconda.org/conda-forge/linux-64/libgcc-devel_linux-64-9.4.0-hd854feb_16.tar.bz2#49d4af017741e08423d1009cb547f80e
-https://conda.anaconda.org/conda-forge/linux-64/libgfortran-3.0.0-1.tar.bz2#d7c7e92a8ccc518709474dd3eda896b9
+https://conda.anaconda.org/conda-forge/linux-64/libgcc-devel_linux-64-9.5.0-h367e8d2_16.tar.bz2#b2f784aca08d3e45288c8ea6c7602b86
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-https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-devel_linux-64-9.4.0-hd854feb_16.tar.bz2#d1421e969cb4f032c0a17da76cf0a375
+https://conda.anaconda.org/conda-forge/linux-64/libstdcxx-devel_linux-64-9.5.0-h367e8d2_16.tar.bz2#e5cfd476f10829efccf955635377cfba
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 https://conda.anaconda.org/conda-forge/linux-64/mscorefonts-0.0.1-2.tar.bz2#c9fd57fc9f2c51ff7b049b64fba8a7df
-https://conda.anaconda.org/main/noarch/tzdata-2022a-hda174b7_0.tar.bz2#a99750e9650510d276b56d2b000f4569
+https://conda.anaconda.org/conda-forge/noarch/tzdata-2022d-h191b570_0.tar.bz2#456b5b1d99e7a9654b331bcd82e71042
 https://conda.anaconda.org/main/noarch/fonts-anaconda-1-h8fa9717_0.tar.bz2#7a445a2d9fbe2a88de8f09e9527f4ce1
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@@ -28,10 +27,9 @@ https://conda.anaconda.org/main/noarch/fonts-conda-ecosystem-1-hd3eb1b0_0.tar.bz
 https://conda.anaconda.org/conda-forge/linux-64/binutils_linux-64-2.36-hf3e587d_10.tar.bz2#9d5cdbfe24b182d4c749b86d500ac9d2
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-https://conda.anaconda.org/main/linux-64/brotli-1.0.9-he6710b0_2.tar.bz2#bdc971e2a9affb5125b68ad708172dab
 https://conda.anaconda.org/main/linux-64/bzip2-1.0.8-h7b6447c_0.tar.bz2#f52e60deb7f4c82821be9a868e889348
 https://conda.anaconda.org/main/linux-64/c-ares-1.18.1-h7f8727e_0.tar.bz2#62ca289a9704ed465d3324295ef851d9
-https://conda.anaconda.org/conda-forge/linux-64/expat-2.4.8-h27087fc_0.tar.bz2#e1b07832504eeba765d648389cc387a9
+https://conda.anaconda.org/main/linux-64/expat-2.4.9-h6a678d5_0.tar.bz2#d254ca6cf5c657cecd6912b0671379cd
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 https://conda.anaconda.org/main/linux-64/graphite2-1.3.14-h295c915_1.tar.bz2#09fcddfe703ce76b4b2d7dd0b6d2f928
@@ -40,52 +38,53 @@ https://conda.anaconda.org/conda-forge/linux-64/icu-68.2-h9c3ff4c_0.tar.bz2#6618
 https://conda.anaconda.org/conda-forge/linux-64/isa-l-2.30.0-ha770c72_4.tar.bz2#e9f011f428f6a0bba8a2613d7c107b88
 https://conda.anaconda.org/main/linux-64/jpeg-9e-h7f8727e_0.tar.bz2#6e1c0fb5260c590f7ef5235cb3d05863
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-https://conda.anaconda.org/main/linux-64/lerc-3.0-h295c915_0.tar.bz2#88199c75f2ac211728febced7785c24e
-https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.10-h7f98852_0.tar.bz2#ffa3a757a97e851293909b49f49f28fb
+https://conda.anaconda.org/conda-forge/linux-64/lerc-4.0.0-h27087fc_0.tar.bz2#76bbff344f0134279f225174e9064c8f
+https://conda.anaconda.org/main/linux-64/libbrotlicommon-1.0.9-h5eee18b_7.tar.bz2#787927eff72e62c270f614cbcba9479c
+https://conda.anaconda.org/conda-forge/linux-64/libdeflate-1.13-h166bdaf_0.tar.bz2#4b5bee2e957570197327d0b20a718891
 https://conda.anaconda.org/main/linux-64/libev-4.33-h7f8727e_1.tar.bz2#eeca774c6154c49340dd403b1928d5e9
-https://conda.anaconda.org/main/linux-64/libffi-3.4.2-h295c915_4.tar.bz2#9420f780186158fa096601855f2f2b92
-https://conda.anaconda.org/main/linux-64/libiconv-1.16-h7f8727e_2.tar.bz2#a8345526ee5452b2c8de4c5ac5b1c05f
+https://conda.anaconda.org/main/linux-64/libffi-3.3-he6710b0_2.tar.bz2#822b5201dde61bc838072dc5b670c88c
+https://conda.anaconda.org/conda-forge/linux-64/libiconv-1.17-h166bdaf_0.tar.bz2#b62b52da46c39ee2bc3c162ac7f1804d
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-https://conda.anaconda.org/main/linux-64/libopenblas-0.3.20-h043d6bf_1.tar.bz2#61f860d152bd9b7dd57e2ec4dabbdeaf
+https://conda.anaconda.org/conda-forge/linux-64/libopenblas-0.3.21-pthreads_h78a6416_3.tar.bz2#8c5963a49b6035c40646a763293fbb35
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@@ -290,4 +289,4 @@ https://conda.anaconda.org/bioconda/osx-64/bioconductor-genefilter-1.76.0-r41h11
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+https://conda.anaconda.org/bioconda/osx-64/bioconductor-deseq2-1.34.0-r41hb890f52_2.tar.bz2#480ff3b340d91e3a4fff6c65a0d22715
diff --git a/conda/environment.yml b/conda/environment.yml
index 3afc17d8..99f0d099 100644
--- a/conda/environment.yml
+++ b/conda/environment.yml
@@ -6,6 +6,7 @@ dependencies:
   - python>=3.9
   - bioconductor-deseq2==1.34.0
   - bowtie==1.3.1
+  - cython==0.29.24
   - fastp==0.23.2
   - htseq==2.0.2
   - nodejs==16.13.1

From 126060699e32b8a80d80fae67025bc04518af8c4 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sat, 1 Oct 2022 16:23:07 -0700
Subject: [PATCH 25/29] setup.sh: Conda will print extra newlines before "done"
 in the "Executing transaction... done" message under certain conditions. The
 installation script checks for this "success string" to confirm
 installation/update since Conda doesn't always return a non-zero exit code on
 failure. The presence of newlines means the pattern fails to match the
 success string. To remedy this, the setup script now removes newlines from
 before checking for the success string.

setup.py:
Very minor cleanup to group Cython Extension record creation under a function
---
 setup.py | 43 ++++++++++++++++++++++---------------------
 setup.sh |  4 ++--
 2 files changed, 24 insertions(+), 23 deletions(-)

diff --git a/setup.py b/setup.py
index d23fdb43..1c9a2da0 100644
--- a/setup.py
+++ b/setup.py
@@ -30,26 +30,27 @@ def in_conda_env(self):
         return all([os.getenv(conda_var) for conda_var in ["CONDA_PREFIX", "CONDA_DEFAULT_ENV"]])
 
 
-pyx_files = [
-    'tiny/rna/counter/stepvector/_stepvector.pyx',
-    'tests/cython_tests/stepvector/test_cython.pyx'
-]
-cxx_extension_args = {
-    'extra_compile_args': ['-stdlib=libc++', '-std=c++11', '-O3'],
-    'extra_link_args': [],
-    'language': 'c++'
-}
-if sys.platform == "darwin":
-    cxx_extension_args['extra_compile_args'] += ['-isystem', '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include']
-    cxx_extension_args['extra_link_args'] += ['-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib']
-cython_extensions = [
-    setuptools.Extension(
-        pyx_filename.replace('/', '.').rstrip('.pyx'),
-        sources=[pyx_filename],
-        **cxx_extension_args
-    )
-    for pyx_filename in pyx_files
-]
+def get_cython_extension_defs():
+    pyx_files = [
+        'tiny/rna/counter/stepvector/_stepvector.pyx',
+        'tests/cython_tests/stepvector/test_cython.pyx'
+    ]
+
+    cxx_extension_args = {
+        'extra_compile_args': ['-std=c++11', '-O3'],
+        'extra_link_args': [],
+        'language': 'c++'
+    }
+
+    if sys.platform == "darwin":
+        cxx_extension_args['extra_compile_args'] += ['-isystem', '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include']
+        cxx_extension_args['extra_link_args'] += ['-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib']
+
+    return [setuptools.Extension(
+                pyx_filename.replace('/', '.').rstrip('.pyx'),
+                sources=[pyx_filename],
+                **cxx_extension_args)
+            for pyx_filename in pyx_files]
 
 setuptools.setup(
     name=NAME,
@@ -71,7 +72,7 @@ def in_conda_env(self):
         ]
     },
     ext_modules=cythonize(
-        cython_extensions,
+        get_cython_extension_defs(),
         compiler_directives={'language_level': '3'},
         gdb_debug=False
     ),
diff --git a/setup.sh b/setup.sh
index 56ead387..40e24b9b 100755
--- a/setup.sh
+++ b/setup.sh
@@ -58,7 +58,7 @@ function setup_environment() {
   # Setup tinyRNA environment using our generated lock file
   status "Setting up $env_name environment (this may take a while)..."
   conda create --file $platform_lock_file --name $env_name 2>&1 | tee "env_install.log"
-  if ! grep -q "Executing transaction: ...working... done" env_install.log; then
+  if ! tr -d \\n < env_install.log | grep -q "Executing transaction: ...working... done"; then
     fail "$env_name environment setup failed"
     echo "Console output has been saved to env_install.log."
     exit 1
@@ -135,7 +135,7 @@ if conda env list | grep -q "$env_name"; then
     echo
     status "Updating $env_name environment..."
     conda update --file $platform_lock_file --name "$env_name" 2>&1 | tee "env_update.log"
-    if ! grep -q "Executing transaction: ...working... done" env_update.log; then
+    if ! tr -d \\n < env_install.log | grep -q "Executing transaction: ...working... done"; then
       fail "Failed to update the environment"
       echo "Check the env_update.log file for more information."
       exit 1

From f745ef2dbc797334e6d160b38831ddc014fb043e Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sat, 1 Oct 2022 17:58:09 -0700
Subject: [PATCH 26/29] Removing _chromvector.pyx. After further testing I
 found that it was not necessary to patch it in order to use the StepVector,
 as I had once thought.

Updated unit_tests_stepvector.py accordingly and also added the Cython native test, since there isn't a clean way I'm aware of for doing this with the unittest module.
---
 tests/unit_tests_stepvector.py               |  32 ++-
 tiny/rna/counter/stepvector/_chromvector.pyx | 259 -------------------
 2 files changed, 20 insertions(+), 271 deletions(-)
 delete mode 100644 tiny/rna/counter/stepvector/_chromvector.pyx

diff --git a/tests/unit_tests_stepvector.py b/tests/unit_tests_stepvector.py
index 05f03106..c72facb5 100644
--- a/tests/unit_tests_stepvector.py
+++ b/tests/unit_tests_stepvector.py
@@ -6,7 +6,7 @@
 
 class StepVectorTests(unittest.TestCase):
 
-    """Does our Cython StepVector accept and return steps as expected?"""
+    """Does our Cython StepVector integrate with HTSeq's GenomicArray, and accept/return steps as expected?"""
 
     def test_genomicarray_with_cython_stepvec(self):
         # Patch the StepVector reference in the HTSeq module and use a GenomicArray
@@ -47,15 +47,16 @@ def test_genomicarray_with_cython_stepvec(self):
             actual = list(gas['chr']['.'].array[iv.start:iv.end].get_steps())
             self.assertEqual(actual, expected)
 
-    def test_compare_to_htseq_steps(self):
-        """Test currently doesn't work (and it won't be easy to get it to work)
+    """Does the Cython StepVector contain the expected steps/coordinates when called from a Cython .pyx file?"""
 
-        This is because HTSeq's StepVector with typecode 'O' handles .add_value() using the
-        apply() function and a local function which copies the set OUT of the StepVector,
-        adds to it, then puts it back. This is exactly the kind of thing that our
-        specialized StepVector was intended to avoid.
-        """
+    def test_native_cython_expected_steps(self):
+        from tests.cython_tests.stepvector.test_cython import main as cython_native_test
+        cython_native_test()
 
+    """Does the Cython StepVector's steps/coordinates match those in HTSeq's StepVector when called from a .py file?"""
+
+    def test_compare_to_htseq_steps(self):
+        # HTSeq setup
         from HTSeq.StepVector import StepVector as hStepVector
         def htseq_add(x):
             y = x.copy()
@@ -65,6 +66,7 @@ def htseq_add(x):
         sv_len = 200
         ours = StepVector.create(length=sv_len)
         theirs = hStepVector.create(length=sv_len, typecode='O')
+        theirs[:] = set()
         
         iv1 = slice(0, 99)
         iv2 = slice(99, 101)
@@ -78,10 +80,16 @@ def htseq_add(x):
         f4 = {'featE', 'featF', 'featG'}
         fs = [f1, f2, f3, f4]
 
-        for iv, feat in zip(ivs, fs):
-            value = feat
-            theirs[iv].apply(htseq_add)
-            ours[iv] += feat
+        for iv, feat_set in zip(ivs, fs):
+            ours[iv] += feat_set
+
+            # Emulating the behavior of ChromVector
+            # Can't add a set to a set; need to add item by item
+            for value in feat_set:
+                theirs[iv].apply(htseq_add)
+
+        for our_step, their_step in zip(ours.get_steps(), theirs.get_steps()):
+            self.assertEqual(our_step, their_step)
 
 
 if __name__ == '__main__':
diff --git a/tiny/rna/counter/stepvector/_chromvector.pyx b/tiny/rna/counter/stepvector/_chromvector.pyx
deleted file mode 100644
index e0429fe5..00000000
--- a/tiny/rna/counter/stepvector/_chromvector.pyx
+++ /dev/null
@@ -1,259 +0,0 @@
-from ._stepvector import StepVector
-from HTSeq._HTSeq import GenomicInterval
-
-cdef class ChromVector(object):
-    """Counting vector covering a chromosome.
-
-    This class supports only the tinyRNA Cython implementation of the
-    HTSeq StepVector
-    """
-
-    cdef public object array
-    cdef public GenomicInterval iv
-    cdef public int offset
-    cdef public bint is_vector_of_sets
-    cdef public str _storage
-    cdef public str typecode
-    cdef public str memmap_dir
-
-    @classmethod
-    def create(cls, GenomicInterval iv, str typecode, str storage, str memmap_dir=""):
-        """Create ChromVector from GenomicInterval
-
-        Args:
-            iv (GenomicInterval): A GenomicInterval describing the chromosome
-              vector.
-            typecode ('d', 'i', 'l', 'b', or 'O'): What kind of data will be
-              stored inside this chromosome vector. 'd' for double, 'i' for int,
-              'l' for long int, 'b' for boolean, 'O' for arbitrary objects
-              (e.g. sets).
-            storage ('step', 'ndarray', or 'memmap'): What kind of storage to
-              use. 'ndarray' is appropriate for short chromosomes and stores
-              each position in the genome into memory. 'memmap' stores all
-              positions, but maps the memory onto disk for larger chromosomes.
-              'step' is a sparse representation similar to CSR matrices whereby
-              only the boundaries between genomic stretches with differing
-              data content are stored - see HTSeq.StepVector.
-            memmap_dir (str): If using 'memmap' storage, what folder to store
-              the memory maps. These can get quite big.
-
-        Returns:
-            An instance of ChromVector with the requested options.
-
-        """
-        ncv = cls()
-        ncv.iv = iv
-        ncv.array = StepVector.create()
-
-        ncv._storage = storage
-        ncv.typecode = typecode
-        # NOTE: As long as autochromosomes in GenomicArray are infinite length
-        # this has pretty limited use, but that might change
-        ncv.offset = iv.start
-        ncv.is_vector_of_sets = False
-        ncv.memmap_dir = memmap_dir
-        return ncv
-
-    @classmethod
-    def _create_view(cls, ChromVector vec, GenomicInterval iv):
-        if iv.length == 0:
-            raise IndexError("Cannot subset to zero-length interval.")
-        v = cls()
-        v.iv = iv
-        v.array = vec.array
-        v.offset = vec.offset
-        v.is_vector_of_sets = vec.is_vector_of_sets
-        v._storage = vec._storage
-        return v
-
-    def extend_to_include(self, iv):
-        if iv.strand != self.iv.strand:
-            raise ValueError(
-                'The new interval must match the current strandedness',
-            )
-
-        # Step 1: extend the interval
-        length = self.iv.length
-        startdiff = max(self.iv.start - iv.start, 0)
-        self.iv.extend_to_include(iv)
-        self.offset = self.iv.start
-
-        # Step 2: extend the array if needed, and shift-copy the old values
-        if self._storage == 'ndarray':
-            if self.typecode != 'O':
-                array = numpy.zeros(shape=(self.iv.length,), dtype=self.typecode)
-            else:
-                array = numpy.empty(shape=(self.iv.length,), dtype=self.typecode)
-                array[:] = None
-            array[startdiff: startdiff + length] = self.array[:]
-        elif self._storage == 'memmap':
-            array = numpy.memmap(
-                shape=(self.iv.length,), dtype=self.typecode,
-                filename=os.path.join(
-                    self.memmap_dir,
-                    self.iv.chrom + self.iv.strand + str(self.iv.start) + '_' \
-                        + str(self.iv.length) + ".nmm"),
-                mode='w+',
-            )
-            array[startdiff: startdiff + length] = self.array[:]
-        else:
-            # The StepVector is created in ChromVector.create without explicit
-            # boundaries, so it's already bound by 0, +inf. So we do not need
-            # to extend it here, but rather just set the slice to the right
-            # value
-            array = self.array
-        self.array = array
-
-    def __getitem__(self, index):
-        """Index or slice the chromosome.
-
-        The index can be a few things:
-        - an integer: get the value of the vector at that chromosome coordinate
-        - a 1-step slice e.g "4:7": get a view of the chromosome region
-          between those coordinates. The array data are not copied.
-        - a GenomicInterval: similar to slices, with the additional choice of
-          strandedness. If this argument is stranded but the chromosome itself
-          is not stranded, a nonstranded view of the chromosome region is
-          returned.
-
-        """
-        cdef slice index_slice
-        cdef long int index_int
-        cdef long int start, stop
-        cdef GenomicInterval iv
-
-        if isinstance(index, int):
-            index_int = index
-            if index_int < self.iv.start or index_int >= self.iv.end:
-                raise IndexError
-            return self.array[index_int - self.offset]
-
-        elif isinstance(index, slice):
-            index_slice = index
-            if index_slice.start is None:
-                start = self.iv.start
-            else:
-                start = index_slice.start
-                if start < self.iv.start:
-                    raise IndexError("start too small")
-
-            if index_slice.stop is None:
-                stop = self.iv.end
-            else:
-                stop = index_slice.stop
-                if stop > self.iv.end:
-                    raise IndexError("stop too large")
-
-            iv = GenomicInterval(self.iv.chrom, start, stop, self.iv.strand)
-
-            if not self.iv.contains(iv):
-                raise IndexError
-            return ChromVector._create_view(self, iv)
-
-        elif isinstance(index, GenomicInterval):
-            if not self.iv.contains(index):
-                raise IndexError
-
-            if self.iv.strand is strand_nostrand and \
-                    index.strand is not strand_nostrand:
-                iv = index.copy()   # Is this correct now?
-                iv.strand = strand_nostrand
-            else:
-                iv = index
-
-            return ChromVector._create_view(self, iv)
-
-        else:
-            raise TypeError("Illegal index type")
-
-    def __setitem__(self, index, value):
-        cdef slice index_slice
-        cdef long int start, stop
-
-        if isinstance(value, ChromVector):
-            if self.array is value.array and value.iv.start == index.start and \
-                    value.iv.end == index.stop and (index.step is None or index.step == 1):
-                return
-            else:
-                raise NotImplementedError(
-                    "Required assignment signature not yet implemented.")
-
-        if isinstance(index, int):
-            self.array[index - self.iv.start] = value
-
-        elif isinstance(index, slice):
-            index_slice = index
-            if index_slice.start is not None:
-                start = index_slice.start
-                if start < self.iv.start:
-                    raise IndexError("start too small")
-            else:
-                start = self.iv.start
-            if index_slice.stop is not None:
-                stop = index_slice.stop
-                if stop > self.iv.end:
-                    raise IndexError("stop too large")
-            else:
-                stop = self.iv.end
-            if start > stop:
-                raise IndexError("Start of interval is after its end.")
-            if start == stop:
-                raise IndexError("Cannot assign to zero-length interval.")
-            self.array[start - self.offset: stop -
-                       self.iv.start: index.step] = value
-
-        elif isinstance(index, GenomicInterval):
-            if index.chrom != self.iv.chrom:
-                raise KeyError("Chromosome name mismatch.")
-            if self.iv.strand is not strand_nostrand and \
-                    self.iv.strand is not self.index.strand:
-                raise KeyError("Strand mismatch.")
-            self.array[index.iv.start - self.iv.start,
-                       index.iv.end - self.iv.start] = value
-        else:
-            raise TypeError("Illegal index type")
-
-    def __iadd__(self, value):
-        if not self.is_vector_of_sets:
-            self.array[self.iv.start - self.offset: self.iv.end -
-                       self.offset].__iadd__(value)
-        else:
-            def addval(x):
-                y = x.copy()
-                y.add(value)
-                return y
-
-            self.apply(addval)
-        return self
-
-    def __iter__(self):
-        return self.values()
-
-    def values(self):
-        return iter(self.array[self.iv.start - self.offset: self.iv.end - self.offset])
-
-    def steps(self):
-        return _HTSeq_internal.ChromVector_steps(self)
-
-    def apply(self, fun):
-        for iv, value in self.steps():
-            self.array[iv.start - self.offset: iv.end -
-                       self.offset] = fun(value)
-
-    def __repr__(self):
-        return "<%s object, %s, %s>" % (self.__class__.__name__, str(self.iv), self._storage)
-
-    def __reduce__(self):
-        assert self.__class__ is ChromVector
-        return(_ChromVector_unpickle,
-               (self.array, self.iv, self.offset, self.is_vector_of_sets, self._storage))
-
-
-def _ChromVector_unpickle(array, iv, offset, is_vector_of_sets, _storage):
-    cv = ChromVector()
-    cv.array = array
-    cv.iv = iv
-    cv.offset = offset
-    cv.is_vector_of_sets = is_vector_of_sets
-    cv._storage = _storage
-    return cv
\ No newline at end of file

From a6fd064af2625234b8552abb1e321c466f853c66 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sat, 1 Oct 2022 18:29:53 -0700
Subject: [PATCH 27/29] Updates added regarding the interchangeability of ID
 and gene_id. Small grammar corrections in the table in README.md, and a
 correction for the "unassigned" class explanation in tiny-plot.md

---
 README.md         | 12 ++++++------
 doc/tiny-count.md |  3 ++-
 doc/tiny-plot.md  |  4 ++--
 3 files changed, 10 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index 57006663..91b7d4df 100644
--- a/README.md
+++ b/README.md
@@ -90,12 +90,12 @@ tiny get-template
 
 ### Requirements for User-Provided Input Files
 
-| Input Type                                                                 | File Extension    | Requirements                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-|----------------------------------------------------------------------------|-------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-| Reference annotations<br/>[(example)](START_HERE/reference_data/ram1.gff3) | GFF3 / GFF2 / GTF | Column 9 attributes (defined as "tag=value" or "tag "):<ul><li>Each feature's `ID` tag is required</li><li>Feature classes can be defined with the `Class` tag. If undefined, the default value \__UNKNOWN_\_ will be used.</li><li>Discontinuous features must be defined with the `Parent` tag whose value is the logical parent's `ID`, or by sharing the same `ID`.</li><li>Attribute values containing commas must represent lists</li><li>All features must be stranded</li><li>See the example link (left) for col. 9 formatting</li></ul> |
-| Sequencing data<br/>[(example)](START_HERE/fastq_files)                    | FASTQ(.gz)        | Files must be demultiplexed.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
-| Reference genome<br/>[(example)](START_HERE/reference_data/ram1.fa)        | FASTA             | Chromosome identifiers (e.g. Chr1): <ul><li>Must match your reference annotation file chromosome identifiers</li><li>Are case sensitive</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                 |
-| Bowtie indexes (optional) <sup>1</sup>                                     | ebwt              | Must be small indexes (.ebwtl indexes are not supported)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
+| Input Type                                                                 | File Extension    | Requirements                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+|----------------------------------------------------------------------------|-------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
+| Reference annotations<br/>[(example)](START_HERE/reference_data/ram1.gff3) | GFF3 / GFF2 / GTF | Column 9 attributes (defined as "tag=value" or "tag "):<ul><li>Each feature must have an `ID` or `gene_id` tag.</li><li>Feature classes can be defined with the `Class` tag. If undefined, the default value \__UNKNOWN_\_ will be used.</li><li>Discontinuous features must be defined with the `Parent` tag whose value is the logical parent's `ID`, or by sharing the same `ID`.</li><li>Attribute values containing commas must represent lists.</li><li>All features must be stranded.</li><li>See the example link (left) for col. 9 formatting.</li></ul> |
+| Sequencing data<br/>[(example)](START_HERE/fastq_files)                    | FASTQ(.gz)        | Files must be demultiplexed.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
+| Reference genome<br/>[(example)](START_HERE/reference_data/ram1.fa)        | FASTA             | Chromosome identifiers (e.g. Chr1): <ul><li>Must match your reference annotation file chromosome identifiers</li><li>Are case sensitive</li></ul>                                                                                                                                                                                                                                                                                                                                                                                                                 |
+| Bowtie indexes (optional) <sup>1</sup>                                     | ebwt              | Must be small indexes (.ebwtl indexes are not supported)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
 
 <br/><sup>1</sup> Bowtie indexes can be created for you. See the [configuration file documentation](doc/Configuration.md#building-bowtie-indexes).
 
diff --git a/doc/tiny-count.md b/doc/tiny-count.md
index de66cce8..1439c635 100644
--- a/doc/tiny-count.md
+++ b/doc/tiny-count.md
@@ -118,6 +118,7 @@ You may encounter the following cases when you have more than one unique GFF fil
 - If a feature is defined in one GFF file, then again but under a different **Alias by...**, then both aliases are retained and treated as a list. All aliases will be present in the `Feature Name` column of the Feature Counts output table. They will be comma separated.
 
 Discontinuous features and feature filtering support:
-- Discontinuous features are supported (as defined by the `Parent` attribute key, or by a shared `ID` attribute value). Rule and alias matches of descendents are merged with the root parent's.
+- Discontinuous features are supported (as defined by the `Parent` attribute key, or by a shared `ID`/`gene_id` attribute value). Rule and alias matches of descendents are merged with the root parent's.
+- If a feature contains both `ID` and `gene_id` attributes, only the value of `ID` is used as the feature's ID.
 - Features can be filtered during GFF parsing by their `source` and/or `type` columns, and these preferences can be specified in the Run Config file. These are inclusive filters. Only features matching the values specified will be retained for selection and listed in the output counts table. An empty list allows all values. See the [parameters documentation](Parameters.md#filters) for information about specifying these filters.
 - If a filtered feature breaks a feature lineage (that is, features chained via the `Parent` attribute), then the highest non-filtered ancestor is designated the root parent. The lineage is maintained transparently but the filtered feature does not contribute to the domains of selection.
\ No newline at end of file
diff --git a/doc/tiny-plot.md b/doc/tiny-plot.md
index a8e890d8..8b60d37a 100644
--- a/doc/tiny-plot.md
+++ b/doc/tiny-plot.md
@@ -70,8 +70,8 @@ Features can have multiple classes associated with them, so it is useful to see
     <img src="../images/plots/class_chart.jpg" width="80%" alt="class_chart with 8 classes"/>
 </p>
 
-#### Class N
-Class **N** represents the percentage of mapped reads that were unassigned. Sources of unassigned reads include:
+#### Class \_UNASSIGNED_
+This category represents the percentage of mapped reads that were unassigned. Sources of unassigned reads include:
 - A lack of features passing selection at alignment loci
 - Alignments which do not overlap with any features
 

From 81aed023a7a42e69ae28aef9587d855924c779ed Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sun, 2 Oct 2022 18:24:21 -0700
Subject: [PATCH 28/29] Reliability improvements for the installation and use
 of build dependencies on macOS.

setup.py:
Now treats the Cython StepVector and tests as optional extensions so that installation doesn't error out when there are unforeseen system incompatibilities. Installation also determines the path to the macOS SDK in a way that will be compatible with conda-build pipelines (if/when we have a bioconda recipe for tinyRNA). Also: better condition checks for determining when we need to search for the SDK, and better comments/docstrings.

setup.sh:
CommandLineTools is now checked for and installed if not present because it is required for the C++ compiler on macOS. This marks another curious exception to the Conda isolation model. As far as I can tell, build dependencies on Linux are already covered by Conda subdependencies.
---
 setup.py | 53 ++++++++++++++++++++++++++++++++++++++++++++++-------
 setup.sh | 16 ++++++++++++++++
 2 files changed, 62 insertions(+), 7 deletions(-)

diff --git a/setup.py b/setup.py
index 1c9a2da0..8875fcf3 100644
--- a/setup.py
+++ b/setup.py
@@ -19,6 +19,10 @@
 
 
 class PrereqAndExec(install):
+    """These checks are performed prior to installation to ensure that this setup routine
+    is only executed within a Conda environment. Users should perform installation via
+    setup.sh, not setup.py."""
+
     def run(self):
         if not self.in_conda_env():
             sys.exit("CRITICAL ERROR: you appear to be installing %s outside of a conda environment.\n" % (NAME,) +
@@ -31,9 +35,14 @@ def in_conda_env(self):
 
 
 def get_cython_extension_defs():
+    """Returns a list of Extension objects corresponding to the contents of pyx_files.
+    Extensions indicated as optional in pyx_files will NOT cause the installation to
+    error out if there are build issues, and therefore must be used as optional imports."""
+
     pyx_files = [
-        'tiny/rna/counter/stepvector/_stepvector.pyx',
-        'tests/cython_tests/stepvector/test_cython.pyx'
+        # (file path, optional)
+        ('tiny/rna/counter/stepvector/_stepvector.pyx', True),
+        ('tests/cython_tests/stepvector/test_cython.pyx', True)
     ]
 
     cxx_extension_args = {
@@ -42,15 +51,45 @@ def get_cython_extension_defs():
         'language': 'c++'
     }
 
-    if sys.platform == "darwin":
-        cxx_extension_args['extra_compile_args'] += ['-isystem', '/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include']
-        cxx_extension_args['extra_link_args'] += ['-L/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib']
+    if sys.platform == "darwin" and os.getenv('SDKROOT') is None:
+        # If building with the environment variables set by Conda, this isn't necessary
+        # However build shortcuts in some IDEs will strip these vars
+        sdk_root = get_macos_sdk_path()
+        cxx_extension_args['extra_compile_args'] += ['-isystem', os.path.join(sdk_root, '/usr/include')]
+        cxx_extension_args['extra_link_args'] += ['-L' + os.path.join(sdk_root, '/usr/lib')]
 
     return [setuptools.Extension(
-                pyx_filename.replace('/', '.').rstrip('.pyx'),
+                pyx_filename.replace('./', '').replace('/', '.').rstrip('.pyx'),
                 sources=[pyx_filename],
+                optional=optional,
                 **cxx_extension_args)
-            for pyx_filename in pyx_files]
+            for pyx_filename, optional in pyx_files]
+
+
+def get_macos_sdk_path():
+    """Determines the SDK path for compiler dependencies in a manner that will be
+    compatible with conda-build pipelines. The following code was copied from
+    https://github.com/python-pillow/Pillow/blob/main/setup.py """
+
+    try:
+        import subprocess
+        sdk_path = subprocess.check_output(["xcrun", "--show-sdk-path"]).strip().decode('latin1')
+    except Exception:
+        sdk_path = None
+
+    if (
+            not sdk_path
+            or sdk_path == "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk"
+    ):
+        commandlinetools_sdk_path = "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk"
+        if os.path.exists(commandlinetools_sdk_path):
+            sdk_path = commandlinetools_sdk_path
+        else:
+            raise RuntimeError("The macOS SDK path could not be found. This is required for Cython. "
+                               "Please run xcode-select --install in your terminal.")
+
+    return sdk_path
+
 
 setuptools.setup(
     name=NAME,
diff --git a/setup.sh b/setup.sh
index 40e24b9b..8834649c 100755
--- a/setup.sh
+++ b/setup.sh
@@ -67,6 +67,21 @@ function setup_environment() {
   fi
 }
 
+function setup_macOS_command_line_tools() {
+  # Install Xcode command line tools if necessary
+  if ! xcode-select --print-path > /dev/null 2>&1; then
+    status "Installing Xcode command line tools. Follow prompts in new window..."
+    if xcode-select --install; then
+      success "Command line tools setup complete"
+    else
+      fail "Command line tools installation failed"
+      exit 1
+    fi
+  else
+    success "Xcode command line tools are already installed"
+  fi
+}
+
 ################################################################################
 # Main Routine
 ################################################################################
@@ -82,6 +97,7 @@ if [[ "$OSTYPE" == "darwin"* ]]; then
   shell=$(basename "$(dscl . -read ~/ UserShell | cut -f 2 -d " ")")
   miniconda_installer="Miniconda3-py${python_version/./}_${miniconda_version}-MacOSX-x86_64.sh"
   platform_lock_file="./conda/conda-osx-64.lock"
+  setup_macOS_command_line_tools
 elif [[ "$OSTYPE" == "linux-gnu" ]]; then
   success "Linux detected"
   shell="$(basename "$SHELL")"

From 68840196dfad62376da685436ca19ff557a19131 Mon Sep 17 00:00:00 2001
From: Alex Tate <0xalextate@gmail.com>
Date: Sun, 2 Oct 2022 18:34:19 -0700
Subject: [PATCH 29/29] ReferenceTables no longer treats Cython StepVector
 import errors as hard errors, and instead falls back to using HTSeq's
 StepVector. This is because setup.py has been changed to skip installation of
 extensions that produce build errors.

Minor correctness change to the --step-vector command line option (is now --stepvector). Also cleaned up get_macos_sdk_path() in setup.py
---
 doc/Parameters.md               |  6 +++---
 setup.py                        |  9 ++++-----
 tiny/rna/counter/counter.py     |  2 +-
 tiny/rna/counter/hts_parsing.py | 14 ++++++++------
 4 files changed, 16 insertions(+), 15 deletions(-)

diff --git a/doc/Parameters.md b/doc/Parameters.md
index d870c454..b8ca2d63 100644
--- a/doc/Parameters.md
+++ b/doc/Parameters.md
@@ -93,9 +93,9 @@ The SAM files produced by the tinyRNA pipeline are collapsed by default; alignme
 You can optionally filter features in your GFF files by specifying sources and/or types that are desired. Source and type refer to GFF columns 2 and 3 respectively. If source _and_ type filters are specified, each feature must match one of the sources _and_ one of the types in order to be included in the counting process. For both filters, an empty list is the same as "allow all."
 
 ### StepVector
- | Run Config Key     | Commandline Argument |
+| Run Config Key     | Commandline Argument |
 |--------------------|----------------------|
-| counter_stepvector | `--step-vector`      |
+| counter_stepvector | `--stepvector`       |
 
 A custom Cython implementation of HTSeq's StepVector is used for finding features that overlap each alignment interval. While the core C++ component of the StepVector is the same, we have found that our Cython implementation can result in runtimes up to 50% faster than HTSeq's implementation. This parameter allows you to use HTSeq's StepVector if you wish (for example, if the Cython StepVector is incompatible with your system)
 
@@ -153,7 +153,7 @@ Optional arguments:
   -dc, --decollapse     Create a decollapsed copy of all SAM files listed in
                         your Samples Sheet. This option is ignored for non-
                         collapsed inputs.
-  -sv {Cython,HTSeq}, --step-vector {Cython,HTSeq}
+  -sv {Cython,HTSeq}, --stepvector {Cython,HTSeq}
                         Select which StepVector implementation is used to find
                         features overlapping an interval.
   -md, --multi-id       Don't treat features with multiple ID values as an
diff --git a/setup.py b/setup.py
index 8875fcf3..0f83abb4 100644
--- a/setup.py
+++ b/setup.py
@@ -77,11 +77,10 @@ def get_macos_sdk_path():
     except Exception:
         sdk_path = None
 
-    if (
-            not sdk_path
-            or sdk_path == "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk"
-    ):
-        commandlinetools_sdk_path = "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk"
+    xcode_sdk_path = "/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk"
+    commandlinetools_sdk_path = "/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk"
+
+    if not sdk_path or sdk_path == xcode_sdk_path:
         if os.path.exists(commandlinetools_sdk_path):
             sdk_path = commandlinetools_sdk_path
         else:
diff --git a/tiny/rna/counter/counter.py b/tiny/rna/counter/counter.py
index 37329760..c81336d9 100644
--- a/tiny/rna/counter/counter.py
+++ b/tiny/rna/counter/counter.py
@@ -51,7 +51,7 @@ def get_args():
     optional_args.add_argument('-dc', '--decollapse', action='store_true',
                                help='Create a decollapsed copy of all SAM files listed in your '
                                     'Samples Sheet. This option is ignored for non-collapsed inputs.')
-    optional_args.add_argument('-sv', '--step-vector', choices=['Cython', 'HTSeq'], default='Cython',
+    optional_args.add_argument('-sv', '--stepvector', choices=['Cython', 'HTSeq'], default='Cython',
                                help='Select which StepVector implementation is used to find '
                                     'features overlapping an interval.')
     optional_args.add_argument('-md', '--multi-id', action='store_true',
diff --git a/tiny/rna/counter/hts_parsing.py b/tiny/rna/counter/hts_parsing.py
index 533983bf..cccbdce4 100644
--- a/tiny/rna/counter/hts_parsing.py
+++ b/tiny/rna/counter/hts_parsing.py
@@ -446,17 +446,18 @@ def __init__(self, gff_files: Dict[str, list], feature_selector, **prefs):
         self._set_filters(**prefs)
         self.gff_files = gff_files
         # ----------------------------------------------------------- Primary Key:
-        if prefs['step_vector'] == 'Cython':
+        if prefs['stepvector'] == 'Cython':
             try:
                 from tiny.rna.counter.stepvector import StepVector
                 setattr(HTSeq.StepVector, 'StepVector', StepVector)
                 self.feats = HTSeq.GenomicArray("auto", stranded=False)     # Root Match ID
             except ModuleNotFoundError:
-                print("The Cython StepVector has not yet been built.\n"
-                      "Run: python setup.py build_ext --inplace",
+                prefs['stepvector'] = 'HTSeq'
+                print("Failed to import Cython StepVector\n"
+                      "Falling back to HTSeq's StepVector",
                       file=sys.stderr)
-                sys.exit(1)
-        else:
+
+        if prefs['stepvector'] == 'HTSeq':
             self.feats = HTSeq.GenomicArrayOfSets("auto", stranded=False)   # Root Match ID
 
         self.parents, self.filtered = {}, set()                         # Original Feature ID
@@ -701,7 +702,8 @@ def chrom_vector_setdefault(self, chrom):
             self.feats.add_chrom(chrom)
 
     def get_feature_id(self, row):
-        id_collection = row.attr.get('ID', row.attr.get('gene_id', None))
+        id_collection = row.attr.get('ID', default=
+            row.attr.get('gene_id', default=None))
 
         if id_collection is None:
             raise ValueError(f"Feature {row.name} does not contain an ID attribute.")