rebase stale branch to resume development#20

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scharch wants to merge 66 commits intoumiProcessingfrom

Commits on May 20, 2020

many many changes to implement single cell lineage assignment
Chaim Schramm
committed

Commits on Jun 12, 2020

switched 2.4 over to AIRR-tsv input/output only
Chaim Schramm
committed

Commits on Jul 3, 2020

Added preserve option to 2.4
Chaim Schramm
committed
Made filtering rules a little saner and split filtering utility from fasta extractor
Chaim Schramm
committed
minor bug fix
Chaim Schramm
committed
tweaked alignment parameters for 2.1
Chaim Schramm
committed

Commits on Jul 16, 2020

added gene clusterting for lineage analysis
Chaim Schramm
committed

Commits on Jul 17, 2020

fixes to prevent carriage returns
Chaim Schramm
committed
Added complete_vdj flag
Chaim Schramm
committed
Added short names for tracking multiple repertoires
Chaim Schramm
committed
Added short names option to 2.4
Chaim Schramm
committed
reminder to self
Chaim Schramm
committed

Commits on Jul 28, 2020

a bunch of minor fixes
Chaim Schramm
committed

Commits on Sep 25, 2020

minor bug fix
Chaim Schramm
committed

Commits on Oct 23, 2020

several improvements to single cell and multi-file clustering
Chaim Schramm
committed

Commits on Nov 16, 2020

catch an edge case
Chaim Schramm
committed

Commits on Dec 4, 2020

fixes #12
Chaim Schramm
committed

Commits on Feb 17, 2021

allow non-numeric clones in 2.4
Chaim Schramm
committed
minor fixes
Chaim Schramm
committed

Commits on May 13, 2021

bug fix
Chaim A Schramm
committed
added option to extract other rearrangement fields as ID
Chaim A Schramm
committed
add "paired" option to filter levels
Chaim A Schramm
committed

Commits on Jul 20, 2021

tweaked calculation of complete_vdj flag
Chaim A Schramm
committed

Commits on May 17, 2022

changes for how multiplot interacts with ggsave, apparently
Chaim A Schramm
committed
go back to expecting numeric clone IDs; figure out more general solution later.
Chaim A Schramm
committed
more options for --geneClusters
Chaim A Schramm
committed

Commits on Jul 15, 2022

Added threading option to 1.4
Chaim A Schramm
committed
minor fixes
Chaim A Schramm
committed
quotation marks (fixes #4)
Chaim A Schramm
committed
changed single cell default id threshold
Chaim A Schramm
committed
minor readability change to lineage table in geneCluster mode
Chaim A Schramm
committed
added --species option to 2.1
Chaim A Schramm
committed
added networkx to prereqs and rationalized setup messages
Chaim A Schramm
committed
updated README
Chaim A Schramm
committed
Merge pull request #16 from scharch/update2.4
scharch
authored

Commits on Jul 20, 2022

minor fix for bulk sequencing
Chaim A Schramm
committed

Commits on Jul 28, 2022

fixes #17
Chaim A Schramm
committed

Commits on Sep 15, 2022

Commits on Oct 28, 2022

Commits on Nov 29, 2022

Fix bug in handling --noFallBack
scharch
authored

Commits on Jun 2, 2023

catch any error instead of type only
scharch
authored

Commits on Jan 10, 2025

Commits on Jan 30, 2025

change error to warning
scharch
committed

Commits on Jan 31, 2025

updated requirements
scharch
committed

Commits on Jun 5, 2025

Commits on Jul 11, 2025

Commits on Sep 25, 2025