STAR 2.7.11b --- 2024/01/24 ::: Minor in one parameter.

• Replaced --quantTranscriptomeBan parameter with --quantTranscriptomeSAMoutput with more explicit naming of options. The default behavior is not affected.
• New option: --quantTranscriptomeSAMoutput BanSingleEnd_ExtendSoftclip : prohibit single-end alignments, extend softclips, allow indels.

STAR 2.7.11a --- 2023/08/15 ::: STARdiploid

• Implemented STARdiploid option --genomeTransformType Diploid that generates personal diploid genome. At the mapping step, --genomeTransformOutput options will transform the alignments into reference genome coordinates.
• Implemented --soloCBtype String option for arbitrary cell barcode strings without passlist.
• Implemented STARsolo BAM tag sF, which outputs the feature type and number of genes for each read.
• Fixed a GstrandBit issue for the on-the-fly insertion of extra genomic sequences.
• Issue #1909: Fixed a bug causing wrong sequence length in the UB SAM tag for --soloType CB_UMI_Complex.
• Issue #1871: Fixed a bug which occurs when --soloCellReadStats Standard --twopassMode Basic are used together.
• Issue #1763: Fixed a bug causing segnmentation fault in rare cases for 2-pass mapping.
• Issue #1733: Fixed the issue with counting of intronicAS reads in STARsolo CellReads.stats output with --soloFeatures GeneFull_Ex50pAS option.
• Behavior change: for --wasp* ouput, the homozygous SNVs are filtered out from the VCF file.

Bug-fix: STAR_2.7.10b_alpha_23-06-09

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

Bug-fix: STAR_2.7.10b_alpha_230301

Issue #1763: Fixed a bug causing seg-faults in rare cases for 2-pass mapping.

Bug-fix: STAR_2.7.10b_alpha_230111

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

STAR 2.7.10b --- 2022/11/01 ::: Bug-fix release.

• PR #1638: Increased entropy of shmKey to avoid collisions between genomes. Many thanks to Jeff Hussmann (@jeffhussmann).
• Issue #1577: Reduced RAM usage for large STARsolo runs.
• Issue #1612: fixed the problem with Solo.out/SJ/raw/features.tsv sym-link.
• Issues #1469, #1602, #1608: fixed seg-faults introduced in 2.7.10a.
• Issue #1619: fixed memory leak in SoloFeature_cellFiltering.cpp
• Issue #1543: fixed a segfault occurring for STARsolo multimappers and large number of reads per cell.
• Issue #1558: fixed a bug with output of GX/GN BAM tags without CB/UB.
• Issue #1513: if --soloMultiMappers options are not requested, output "NoMulti" in the "Reads Mapped to Gene: Unique+Multiple Gene" line of the Summary.csv file.
• Issue #719: implemented auto re-allocation of the SJ output buffer.
• Fixed a bug with --soloMultiMappers for small number of cells cases.
• Fixed a problem with STARsolo CellReads.stats output for no-passlist runs.

Bug-fix: STAR_2.7.10a_alpha_220818

• Fixed potential seg-fault in STARsolo
• #1619: fixed memory leak in SoloFeature_cellFiltering.cpp

Bug-fix alpha: 2.7.10a_alpha_220601

• Issue #1543: Fixed a segfault occurring for STARsolo multimappers and a large number of reads per cell.
• PR #1550: Add missing #include (GCC 12)

Bug-fix alpha: 2.7.10a_alpha_220517

• Issue #1558: Fixed a bug with the output of GX/GN BAM tags without CB/UB.

Bug-fix alpha: 2.7.10a_alpha_220506

• Fixed a bug with --soloMultiMappers for small number of cells cases.
• Issue #1513: If --soloMultiMappers options are not requested, output "NoMulti" in the "Reads Mapped to Gene: Unique+Multiple Gene" line of the Summary.csv file.