Convert the submodule star-sys/STAR to a git subtree#29

Merged

sjackman merged 594 commits intomasterfrom sj/subtree

Aug 14, 2020

+63,279-5

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Commits on Dec 1, 2017

Passes chr22 TestSuite tests.
alexdobin
committed

Commits on Dec 4, 2017

Merged master changes in to var.
alexdobin
committed

Commits on Dec 7, 2017

Implemented --readFilesPrefix option for specifying prefix (e.g. directory path) for the file names in --readFilesIn . Implemented read group ID output as the last column of the Chimeric.out.juncti…
alexdobin
committed
Merge pull request #334 from drpowell/master
alexdobin
authored

Commits on Dec 18, 2017

Merged master changes (RG for chimeric junction output) into var.
alexdobin
committed

Commits on Dec 21, 2017

Commits on Dec 22, 2017

Commits on Dec 28, 2017

Implementing WASP algorithm.
alexdobin
committed

Commits on Jan 1, 2018

Added variant allele=4 for variant read base=N. Added various waspType values.
alexdobin
committed

Commits on Jan 3, 2018

Initial test release of WASP filtering.
alexdobin
committed

Commits on Jan 5, 2018

For BAM to signal conversion, process alignments without NH tags as unique (i.e. NH=1).
alexdobin
committed

Commits on Jan 9, 2018

Implemented --outBAMsortingBinsN option to control the number of sorting bins. Icnreasing this number reduces the amount of RAM required for sorting.
alexdobin
committed

Commits on Jan 17, 2018

Fixed vW:i:2 type to mark multimappers that overlap variants. Recompiled executables.
alexdobin
committed

Commits on Jan 23, 2018

2.5.4a
alexdobin
committed

Commits on Jan 25, 2018

Commits on Jan 26, 2018

spelling fixes
satta
committed

Commits on Jan 29, 2018

Implemented merging and re-mapping for overlapping mates. To control it, use --peOverlapNbasesMin and --peOverlapMMp oprions.
alexdobin
committed

Commits on Feb 9, 2018

2.5.4b
alexdobin
committed

Commits on Feb 25, 2018

Fixed a problem in the chimeric detection algorithm for overlapping PE reads.
alexdobin
committed

Commits on Mar 13, 2018

Commits on Mar 19, 2018

Fixed a bug in the overlapping mates algorithm.
alexdobin
committed

Commits on Mar 22, 2018

Fixed a bug in the overlapping mates algorithm related to protruding ends of the mates.
alexdobin
committed

Commits on Mar 26, 2018

Commits on Mar 30, 2018

Fixed problems with merged PE chimeric output.
alexdobin
committed

Commits on Apr 6, 2018

Commits on Apr 11, 2018

Commits on Apr 20, 2018

--chimScoreJunctionNonGTAG is now added to chimeric score for thresholding with --chimScoreMin and --chimScoreDropMax; large negative number will prohibit non-GTAG chimeric junctions. Fixed a bug i…
alexdobin
committed

Commits on Apr 23, 2018

Commits on Apr 26, 2018

Fixed a bug that accidentally turns on --peOverlap* option and causes seg-fault.
alexdobin
committed

Commits on May 2, 2018

Commits on May 3, 2018

Fixed another bug in the peOverlap algorithm.
alexdobin
committed

Commits on May 7, 2018

Fixed the problem with Ns in the overlap region for the peOverlap algorithm.
alexdobin
committed

Commits on May 10, 2018

Fixed problems with WASP filtering.
alexdobin
committed

Commits on Jun 14, 2018

Commits on Jul 13, 2018

Fixed the problem with alignment scoring with peOverlap option which may cause seg-faults in rare cases.
alexdobin
committed

Commits on Jul 20, 2018

Fixed another problem with alignment scoring with peOverlap option which may cause seg-faults in rare cases.
alexdobin
committed

Commits on Aug 9, 2018

Fixed a bug with multiple RG lines when inputting reads in SAM format. Fixed a bug causing seg-faults with sharead memory and --outStd options.
alexdobin
committed

Commits on Aug 12, 2018

Fixed the problem with control characters (ASCII<32) in genome and input read sequences. They used to be converted to N, now they are removed. Fixed the GtstrandBit problem. Another attempt to fix …
alexdobin
committed

Commits on Aug 13, 2018

Implemented --chimOutJunctionFormat 1 option to output some metadata (command lines and basic mapping statistics) at the end of Chimeric.out.junction file. Fixed a bug in merging mates (--peOverlap…
alexdobin
committed

Commits on Aug 14, 2018

Commits on Aug 18, 2018

fix spelling issues
satta
committed

Commits on Aug 27, 2018

Fixed a problem with --outSAMfilter KeepOnlyAddedReferences option. Fixed a problem with output of an empty sorted BAM.
alexdobin
committed

Commits on Sep 6, 2018

Preparing for 2.6.1b
alexdobin
committed

Commits on Oct 1, 2018

Enforced the consistent choice of supplementary chimeric alignments for overlapping mates.
alexdobin
committed

Commits on Oct 3, 2018

Commits on Oct 5, 2018

Implementing solo.
alexdobin
committed

Commits on Oct 17, 2018

Preparing for 2.6.1c
alexdobin
committed

Commits on Oct 22, 2018

Solo: CB matching to whitelist.
alexdobin
committed

Commits on Oct 27, 2018

Commits on Oct 29, 2018

Implementing gene from transcript alignment
Alexander Dobin
committed
Implementing gene from transcript alignment 2
Alexander Dobin
committed

Commits on Oct 30, 2018

Fixed the bug causing inconsistent output for mate1/2 in the Unmapped files.
alexdobin
committed
Solo: implemented gene from transcripts.
Alex Dobin
committed
Solo: implementing post-map aggregation.
Alex Dobin
committed

Commits on Nov 3, 2018

Implementing UMI collapsing.
alexdobin
committed

Commits on Nov 5, 2018

Commits on Nov 6, 2018

Implementing UMI collapsing with 1MM
alexdobin
committed

Commits on Nov 7, 2018

Implemented UMI collapsing with 1MM
alexdobin
committed

Commits on Dec 15, 2018

Fixing bugs in solo.
alexdobin
committed

Commits on Dec 17, 2018

Allowed Ns in CBs in accordance with CellRanger pipeline.
alexdobin
committed

Commits on Dec 22, 2018

Commits on Dec 23, 2018

Commits on Dec 29, 2018

Added gene name and biotype output, and gene output for splice junctions.
alexdobin
committed

Commits on Dec 31, 2018

Commits on Jan 9, 2019

Preliminary STARsolo release.
alexdobin
committed

Commits on Jan 15, 2019

Default transcriptome conversion options for STARsolo.
alexdobin
committed

Commits on Jan 17, 2019

Commits on Jan 22, 2019

Final changes for solo* parameters.
alexdobin
committed

Commits on Jan 23, 2019

Commits on Jan 24, 2019

2.7.0a
alexdobin
committed

Commits on Jan 25, 2019

header needed for python scipy mmread compatibility
k3yavi
authored

Commits on Jan 29, 2019

Just a final blank in a Makefile
smoe
authored

Commits on Feb 4, 2019

Commits on Feb 5, 2019

Ready for 2.7.0b
alexdobin
committed

Commits on Feb 6, 2019

Commits on Feb 7, 2019

Fixed a problem with STARsolo genes.tsv output.
alexdobin
committed

Commits on Feb 8, 2019

Ready for 2.7.0c
alexdobin
committed

Commits on Feb 13, 2019

Enforced genome version rules for 2.7.0
alexdobin
committed

Commits on Feb 17, 2019

* Implemented --soloBarcodeReadLength option for barcode read length not equal to the UMI+CB length.
alexdobin
committed

Commits on Feb 18, 2019

Commits on Feb 19, 2019

Started implementing STARsolo GeneFull option.
alexdobin
committed

Commits on Feb 20, 2019

Commits on Feb 21, 2019

Commits on Feb 22, 2019

Fixed problem in gene info input.
alexdobin
committed

Commits on Feb 25, 2019

Commits on Mar 7, 2019

Minor text fixes in parametersDefault.
alexdobin
committed

Commits on Mar 14, 2019

Fixed problems with STARsolo and 2-pass.
alexdobin
committed

Commits on Mar 15, 2019

Commits on Mar 18, 2019

Allow same tag for "--sjdbGTFtagExonParentTranscript" and "--sjdbGTFtagExonParentGene".
ghuls
committed

Commits on Mar 19, 2019

Implemented no-whitelist solo operation.
alexdobin
committed

Commits on Mar 20, 2019

Commits on Mar 22, 2019

Fixed a problem in STARsolo with empty Unmapped.out.mate2 file. Issue #593.
alexdobin
committed

Commits on Mar 25, 2019

Commits on Mar 27, 2019

Fixed several problems with previous changes.
alexdobin
committed

Commits on Mar 28, 2019

Commits on Mar 30, 2019

Commits on Apr 5, 2019

Commits on Apr 8, 2019

Commits on Apr 10, 2019

Commits on Apr 11, 2019

Commits on Apr 29, 2019

Stratified the GTF gene ID/name/type and transcript ID loading to safely process missing fields.
alexdobin
committed

Commits on May 1, 2019

2.7.0f_solo_GeneFull_0430
alexdobin
committed

Commits on May 14, 2019

Added collapsing of CB in whitelist. Added output of unmapped read numbers to Log.final.out. Fixed a problem with --quantMode TranscriptomeSAM and --twopassMode Basic.
alexdobin
committed

Commits on May 21, 2019

Implemented extras/scripts/soloBasicCellFilter.awk script to perform basic filtering of the STARsolo count matrices.
alexdobin
committed

Commits on Jun 19, 2019

Fixed the problem with ALT=* in STAR-WASP.
alexdobin
committed

Commits on Aug 7, 2019

Commits on Aug 9, 2019

use mergedPE align score for comparison w/ chimeric mergedPE score
brianjohnhaas
committed

Commits on Aug 12, 2019

Added header to Chimeric.out.junction. Remove all parameters output from Log.out.
alexdobin
committed

Commits on Aug 13, 2019

Commits on Jan 3, 2020

Initial orbit commit

michael.kirsche
authored and
Lance Hepler
committed
Removed deprecated print statements, added current output

michael.kirsche
authored and
Lance Hepler
committed
Added orbit.h which includes extern C for main API, refactored methods a bit

michael.kirsche
authored and
Lance Hepler
committed
Fixed a few bugs, and added a new barrage of commented-out print statements

michael.kirsche
authored and
Lance Hepler
committed
Update orbit c++ building config

michael.kirsche
authored and
Lance Hepler
committed
Removed compiled static libraries

michael.kirsche
authored and
Lance Hepler
committed
Updated Makefile to actually work with liborbit.a

michael.kirsche
authored and
Lance Hepler
committed
Updates and removing useless stuff and bug fixes galore

michael.kirsche
authored and
Lance Hepler
committed
Return pointer instead of string object to avoid memory issues

michael.kirsche
authored and
Lance Hepler
committed
Removed leftover omp stuff

michael.kirsche
authored and
Lance Hepler
committed
Constification of mapGen

michael.kirsche
authored and
Lance Hepler
committed
Simplified Makefile

michael.kirsche
authored and
Lance Hepler
committed
Updated output to not include a dummy read name

michael.kirsche
authored and
Lance Hepler
committed
Remove extra print statements

michael.kirsche
authored and
Lance Hepler
committed
Added support to API for read pair alignment

michael.kirsche
authored and
Lance Hepler
committed
Added support for cloning an aligner

michael.kirsche
authored and
Lance Hepler
committed
Removing unneeded print statements

michael.kirsche
authored and
Lance Hepler
committed
Updated makefile to default to liborbit.a, removed tmp directory creation in

michael.kirsche
authored and
Lance Hepler
committed
Added comments to main orbit source files to document what they do

michael.kirsche
authored and
Lance Hepler
committed
Made parameters const and updated APIs to separate information shared between

michael.kirsche
authored and
Lance Hepler
committed
Removed debug print statement

michael.kirsche
authored and
Lance Hepler
committed
Updated destructors to make sense with aligners initialized from a reference

michael.kirsche
authored and
Lance Hepler
committed
Fixed a few bugs that came up when running multiple instances in parallel

michael.kirsche
authored and
Lance Hepler
committed
Bug fix

michael.kirsche
authored and
Lance Hepler
committed
Add destructor for OutSJ

michael.kirsche
authored and
Lance Hepler
committed
Cleaned up some comments

michael.kirsche
authored and
Lance Hepler
committed
build on Mac

pmarks
authored and
Lance Hepler
committed
don't make the huge SJ output vec

pmarks
authored and
Lance Hepler
committed
Fix small memory leak (inspire by f0cadaf)
Lance Hepler
committed
Workaround for problems with older libc.

adam-azarchs
authored and
Lance Hepler
committed
More workarounds for old glibc bug with strtoul.

adam-azarchs
authored and
Lance Hepler
committed
More signed/unsiged fixes.

adam-azarchs
authored and
Lance Hepler
committed
Fix use of nonstandard istringstream buffer API.

adam-azarchs
authored and
Lance Hepler
committed
Fix output buffer initialization.

adam-azarchs
authored and
Lance Hepler
committed
Free the memory of the reference genome (#3 )

sjackman
authored and
Lance Hepler
committed
fix resource cleanup code
Lance Hepler
committed
make logging a no-op
Lance Hepler
committed
fix whitespace issues cause by lack of vim config
Lance Hepler
committed

Commits on Jan 14, 2020

orbit: fix memory leak
Lance Hepler
committed
orbit: fix missing includes
Lance Hepler
committed

Commits on Jan 15, 2020

Genome: fix use (delete[]) after free
Lance Hepler
committed

Commits on Jan 16, 2020

fix other memleak
Lance Hepler
committed

Commits on Feb 2, 2020

trim links to unused code
pmarks
committed

Commits on Apr 26, 2020

fixes for paired-end support
Lance Hepler
committed

Commits on Apr 27, 2020

new interface requires fewer mallocs per alignment
Lance Hepler
committed

Commits on Jul 13, 2020

re-instate reference version check
Lance Hepler
committed

Commits on Jul 14, 2020

forfeit STARsolo to bring back quantMode
Lance Hepler
committed