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Commits on May 28, 2024

• add back the option to only annotate CR/UR

  Yichen-Si

  committedMay 28, 2024
  6709b91

Commits on May 27, 2024

• integrate barcode annotation with solo counting

  Yichen-Si

  committedMay 27, 2024
  734895d

Commits on May 23, 2024

• barcode error correction & annotate spatial coordinates

  Yichen-Si

  committedMay 23, 2024
  a99311c

Commits on May 21, 2024

• initial test for the case where one input fastx contains only barcode

  Yichen-Si

  committedMay 21, 2024
  e08655c

Commits on Jan 25, 2024

• Ready for 2.7.11b

  alexdobin

  committedJan 25, 2024
  73eaeb2

• Merge branch 'patch-1' of https://github.com/rcannood/STAR

  alexdobin

  committedJan 25, 2024
  a72e5fa

Commits on Dec 22, 2023

• 2.7.11a_Diploid_TrSAMfix. Behavior change: replaced --quantTranscriptomeBan option with --quantTranscriptomeSAMoutput option. New option: --quantTranscriptomeSAMoutput BanSingleEnd_ExtendSoftclip :…

  alexdobin

  committedDec 22, 2023
  326ca13

Commits on Aug 8, 2023

• Preparing 2.7.11a

  alexdobin

  committedAug 8, 2023
  826820c

• Merged STARdiploid branch.

  alexdobin

  committedAug 8, 2023
  40a8d6e

Commits on Jul 24, 2023

• Issue alexdobin#1909: Fixed a bug causing wrong sequence length in the UB SAM tag for --soloType CB_UMI_Complex.

  alexdobin

  committedJul 24, 2023
  148129c

Commits on Jul 19, 2023

• 2.7.10b_alpha_2023-07-19. Finalized --soloCBtype String option for arbitrary cell barcode strings without passlist.

  alexdobin

  committedJul 19, 2023
  fdf7a25

Commits on Jul 18, 2023

• Implemented option for arbitrary cell barcode strings without passlist.

  alexdobin

  committedJul 18, 2023
  c087569

Commits on Jul 6, 2023

• Added STARsolo BAM tag sF, which outputs the feature type and number of genes for each read.

  alexdobin

  committedJul 6, 2023
  f31abdf

Commits on Jun 20, 2023

• 2.7.10b_alpha_23-06-20: Fixed a GstrandBit issue for the on-the-fly insertion of extra genomic sequences.

  alexdobin

  committedJun 20, 2023
  0299f2b

Commits on Jun 9, 2023

• 2.7.10b_alpha_23-06-09: Issue alexdobin#1871: Fixed a bug which occurs when --soloCellReadStats Standard --twopassMode Basic are used together.

  alexdobin

  committedJun 9, 2023
  56c9fd5

Commits on May 2, 2023

• Fixed haplotype tag (ha) for STARdiploid SAM/BAM output.

  alexdobin

  committedMay 2, 2023
  0628ce5

Commits on Mar 24, 2023

• Fixed issues with 2-pass and WASP for diploid genome mapping.

  alexdobin

  committedMar 24, 2023
  f7b9edd

Commits on Mar 9, 2023

• Fixed primary flag for diploid transformation.

  alexdobin

  committedMar 9, 2023
  74d65f6

Commits on Mar 8, 2023

• Finalizing STARdiploid.

  alexdobin

  committedMar 8, 2023
  b4ea237

Commits on Mar 1, 2023

• 2.7.10b_alpha_230301: Issue alexdobin#1763: Fixed a bug causing segnmentation fault in rare cases for 2-pass mapping.

  alexdobin

  committedMar 1, 2023
  45fe3dd

Commits on Jan 11, 2023

• 2.7.10b_alpha_220111: Issue alexdobin#1733: Fixed the issue with counting of intronicAS reads in STARsolo CellReads.stats output with --soloFeatures GeneFull_Ex50pAS option.

  alexdobin

  committedJan 11, 2023
  f4fa8e8

Commits on Dec 12, 2022

• fix more typos

  rcannood

  committedDec 12, 2022
  80125eb

Commits on Nov 22, 2022

• fix typos and uniformise

  rcannood

  committedNov 22, 2022
  1d19930

• further clean up file

  rcannood

  committedNov 22, 2022
  3c17f0b

Commits on Nov 21, 2022

• standardise parameter format

  rcannood

  committedNov 21, 2022
  fed056b

Commits on Oct 20, 2022

• Ready for 2.7.10b

  alexdobin

  committedOct 20, 2022
  c6f8efc

• Rearranged collapseUMIall().

  alexdobin

  committedOct 20, 2022
  6f2442d

• renamed: SoloFeature_collapseUMIall_multiMappers.cpp -> SoloFeature_collapseUMIall.cpp

  alexdobin

  committedOct 20, 2022
  e1a0d39

Commits on Oct 19, 2022

• Reduced RAM usage for large STARsolo runs.

  alexdobin

  committedOct 19, 2022
  e7e8833

Commits on Sep 16, 2022

• Merge branch 'avoid_genome_collisions' of https://github.com/jeffhussmann/STAR into jeffhussmann-avoid_genome_collisions

  alexdobin

  committedSep 16, 2022
  5c3681a

• Issue alexdobin#1645: fixed rare seg-fault for --soloFeature SJ. Issue # 1650: added #include <sys/types.h> to SharedMemory.cpp to fix compilation issue on some systems.

  alexdobin

  committedSep 16, 2022
  5f9ad24

Commits on Aug 31, 2022

• Issue alexdobin#719: implemented auto re-allocation of the SJ output buffer.

  alexdobin

  committedAug 31, 2022
  4ef655b

Commits on Aug 25, 2022

• Issue alexdobin#1612: fixed the problem with Solo.out/SJ/raw/features.tsv sym-link.

  alexdobin

  committedAug 25, 2022
  85f957f

• Increased entropy of shmKey to avoid collisions between genomes.

  jeffhussmann

  committedAug 25, 2022
  4d762b9

Commits on Aug 18, 2022

• Bug-fix alpha: 2.7.10a_alpha_220818

  alexdobin

  committedAug 18, 2022
  5e8a99c

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