tiny-count: selective performance improvements via Cython

MANIFEST.in

@@ -1,4 +1,5 @@
 include README.md
+exclude tests
 graft tiny
 prune **/__pycache__
 prune **/*_Outputs

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).
 

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