All pull requests

Pull requests

• peOverlap EndToEnd: keep the merged read's chromosome-edge transcript

  #377·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• SEQ and Unmapped.out.mate keep the read's letters (lowercase, IUPAC)

  #376·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• NH over all loci, 0x200 from the Illumina filter flag, --outFilterMismatchNoverReadLmax

  #375·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• Refuse a junction or annotation table cut short

  #374·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• alignMatesGapMax limits the gap between mates, not the fragment span

  #373·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• GeneCounts: stranded columns use each exon's strand, as STAR

  #372·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• CellReads.stats rows in whitelist order, not thread order

  #371·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• bamRemoveDuplicates: a mateless unique read keeps the cluster open, as STAR

  #370·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• parity_suite.sh: run on macOS, and flag runs that read no reads

  #369·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• --alignEndsType on pairs: extend a mate's two ends while stitching (100M, AS:182 as STAR)

  #368·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• Half-mapped pairs go through the same selection and filters as pairs

  #367·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• Read loops: one shared per-read output and writer stage

  #366·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• Remove dead code; stdout writers are the file writers on another output

  #365·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• Unmapped.out.mate* names and sequences as STAR writes them

  #364·BenjaminDEMAILLE opened Nov 3, 2026Contributor·

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• bamRemoveDuplicates: stream the BAM cluster by cluster (peak RSS 6.4 GB to 10 MB on 7.6M records, identical bytes)

  #363·BenjaminDEMAILLE opened Nov 2, 2026Contributor·

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• STARsolo UMI dedup: look up 1-mismatch neighbours instead of comparing all pairs (200k UMIs: 44-109 s to 62-208 ms)

  #362·BenjaminDEMAILLE opened Nov 2, 2026Contributor·

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• Window bins capped by the index's genomeChrBinNbits; chimeric place() cannot hang

  #361·BenjaminDEMAILLE opened Nov 2, 2026Contributor·

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• Solo: refuse what the read loops cannot do, check barcode and UMI input

  #360·BenjaminDEMAILLE opened Nov 2, 2026Contributor·

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• Remove stale docs-old/, STAR-RS-COMPARISON.md, test/IMPLEMENTATION_SUMMARY.md; fix README status line

  #359·BenjaminDEMAILLE opened Nov 2, 2026Contributor·

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• FASTA reads, blank lines and mate names as STAR; spill folder; --outBAMcompression -1

  #358·BenjaminDEMAILLE opened Nov 2, 2026Contributor·

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• Junctions near a genome edge, SAindex after a dropped junction, index checks at load

  #357·BenjaminDEMAILLE opened Nov 2, 2026Contributor·

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• GTF parser: refuse an annotation that matches nothing, accept GFF3

  #356·BenjaminDEMAILLE opened Nov 2, 2026Contributor·

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• Write SJ.out.tab when empty, report a failed final SAM write

  #355·BenjaminDEMAILLE opened Nov 2, 2026Contributor·

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• --readFilesCommand takes what STAR takes

  #353·BenjaminDEMAILLE opened Nov 2, 2026Contributor·

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• Streamed FASTQ input: refuse two-pass, make cut streams fail

  #352·BenjaminDEMAILLE opened Nov 2, 2026Contributor·

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