feat: add `--quantMode TranscriptomeSAM` output#4

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ewels wants to merge 17 commits into

feat/run-rng-seedfrom

feat/transcriptome-sam

Commits on Apr 17, 2026

feat(quant): add TranscriptomeIndex built from GTF exon groups

ewels
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claude
committed
feat(quant): project genome alignments onto transcripts (align_to_transcripts)

ewels
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claude
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feat(quant): filter modes + softclip extension for transcriptome SAM

ewels
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claude
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feat(params): --quantTranscriptomeSAMoutput + TranscriptomeSAM validation

ewels
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claude
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feat(io/bam,lib): wire Aligned.toTranscriptome.out.bam pipeline

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claude
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test: integration test for --quantMode TranscriptomeSAM

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chore(simplify): drop dead Display + allow_single_end on QuantTranscriptomeSAMoutput

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chore(simplify): share a single rc_encode helper in transcriptome builders

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claude
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chore(simplify): emit PE transcriptome records with one build call per mate

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claude
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chore(simplify): share primary-hit + MAPQ picker between SE and PE

ewels
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claude
committed
chore(simplify): share BGZF writer setup between BamWriter constructors

ewels
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claude
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chore(simplify): collapse locals in extend_softclips trailing fixup

ewels
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claude
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chore(simplify): tighten filter_and_project docs + drop unread read_seq clone

ewels
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claude
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chore(simplify): fix stale mate_or_junction_before comment in align_to_one_transcript

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chore(simplify): drop speculative BamWriter::header accessor

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chore(simplify): accept IntoIterator in build_transcriptome_records_pe

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chore(simplify): drop redundant StdHashMap alias in transcriptome tests

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claude
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feat: add `--quantMode TranscriptomeSAM` output#4

feat: add `--quantMode TranscriptomeSAM` output#4
ewels wants to merge 17 commits into
feat/run-rng-seedfrom
feat/transcriptome-sam

Commits on Apr 17, 2026

feat(quant): add TranscriptomeIndex built from GTF exon groups

feat(quant): project genome alignments onto transcripts (align_to_transcripts)

feat(quant): filter modes + softclip extension for transcriptome SAM

feat(params): --quantTranscriptomeSAMoutput + TranscriptomeSAM validation

feat(io/bam,lib): wire Aligned.toTranscriptome.out.bam pipeline

test: integration test for --quantMode TranscriptomeSAM

chore(simplify): drop dead Display + allow_single_end on QuantTranscriptomeSAMoutput

chore(simplify): share a single rc_encode helper in transcriptome builders

chore(simplify): emit PE transcriptome records with one build call per mate

chore(simplify): share primary-hit + MAPQ picker between SE and PE

chore(simplify): share BGZF writer setup between BamWriter constructors

chore(simplify): collapse locals in extend_softclips trailing fixup

chore(simplify): tighten filter_and_project docs + drop unread read_seq clone

chore(simplify): fix stale mate_or_junction_before comment in align_to_one_transcript

chore(simplify): drop speculative BamWriter::header accessor

chore(simplify): accept IntoIterator in build_transcriptome_records_pe

chore(simplify): drop redundant StdHashMap alias in transcriptome tests