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Commits on Jan 15, 2022

• 2.7.10a

  alexdobin

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Commits on Jan 14, 2022

• Ready for 2.7.10a

  alexdobin

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Commits on Jan 13, 2022

• Fixed a bug in CB_samTagOut introduced by latest changes.

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• Fixed a bug in Velocyto introduced by latest changes.

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Commits on Jan 12, 2022

• dev_ExonOverIntron_ReadStats_2021-01-12

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• Merge branch 'assign_SA_to_correct_mate_when_mates_fully_overlap' of https://github.com/suhrig/STAR into dev_ExonOverIntron_ReadStats

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• Finalized CellReads statistics output.

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Commits on Jan 6, 2022

• Debugging agreement between CellReadStats and Features.stats.

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Commits on Dec 28, 2021

• Output statistics for reads with CB not matching passlist.

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Commits on Dec 23, 2021

• Fixed discrepancies between CellReadStats and BAM.

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Commits on Dec 22, 2021

• Fixed a problem with exonic/intronic read statistics for multimappers.

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Commits on Dec 20, 2021

• Implemented mito read counting for Solo.

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Commits on Dec 17, 2021

• Fixed the problem with Features.stats for multi-gene reads.

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Commits on Dec 16, 2021

• Implemented most of Read statistics. Now need to fix a problem with unique/multi-gene read counting that manifests in Features.stats

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Commits on Dec 14, 2021

• assign supplementary alignment to correct mate when mates fully overlap

  suhrig

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Commits on Dec 8, 2021

• Implementing Read Statistics.

  alexdobin

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• Reverted to normal GeneFull_EoI implementation, renamed the ParseBio_ED3 option into EditDist_3.

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Commits on Dec 3, 2021

• Temporary implementation of GeneFullClosest3p as GeneFull_EoI, will revert in the next commit.

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Commits on Nov 15, 2021

• Switched to max ED=2 for Split-seq data.

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Commits on Oct 26, 2021

• Changed --soloType CB_samTagOut behavior: if barcode cennot be matched to the passlist, CB:Z:- will be recorded (previously CB tag was absent for such reads).

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Commits on Oct 25, 2021

• Fixed a problem with the GeneFull_Ex50pAS option.

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Commits on Oct 20, 2021

• Fixed a problem which results in a slightly different output for Solo SmartSeq after readAnnot.annotFeatures implementation.

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Commits on Oct 4, 2021

• More changes to the statistics output. Now the sum of all values in Solo.out/Barcodes.stats should be equal to total number of reads. The number of all records starting with 'no' in Solo.out/Barcod…

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  alexdobin

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Commits on Oct 1, 2021

• Allow to define --clip5pAdapterSeq with --clipAdapterType CellRanger4 option. Fixed a problem with sym-linking of SJ.out.tab.

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Commits on Sep 30, 2021

• Issues #535, #1350: fixed a long-standing problem that resulted in a seg-fault whem mapping to the rabbit genome. Issue #1223: fixed the N_unmapped value reported in ReadsPerGene.out.tab. The singl…

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Commits on Sep 27, 2021

• Issue #843: for comma separated list of input files in --readFilesIn, check every file for access.

  alexdobin

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• Issue #1322: for incorrectly formatted read lines, output the offending read number and line.

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Commits on Sep 24, 2021

• Issue 1339: clarified the --soloCellFilter EmptyDrops_CR warning message in case the *true empty* cells cannot be found.

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• Issue #1316: fixed the seg-fault which occurred if --soloType CB_samTagOut and --soloCBwhitelist None are used together.

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Commits on Sep 22, 2021

• Changed Solo summary statistics outputs in Barcodes.stats and Features.stats files.

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• Implemented --soloCBmatchWLtype ParseBio_ED3 to allow multiple mismatches and one insertion+deletion for --soloType CB_UMI_Complex.

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Commits on Sep 20, 2021

• Implemented simple insertions, but it seems we need insertion/deletion combinations.

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Commits on Sep 15, 2021

• Implemented Solo BAM tags gx gn: output ';'-separated gene IDs and names for both unique- and multi-gene reads. Note that GX/GN tags are used to output gene ID/name for unique-gene reads.

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• Changed Solo BAM tags output for multiple --soloFeatures: now the first feature on the list is used for GX,GN,XB,UB tags.

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Commits on Sep 14, 2021

• Rearranging output of different features.

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