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3176c7e
feat: add --runRNGseed and seeded primary tie-break
ewels Apr 17, 2026
6740954
Add --outSAMattrRGline flag and emit @RG header + RG:Z tags
ewels Apr 17, 2026
2fe0aa9
chore(simplify): use SliceRandom::shuffle for tied-prefix shuffle
ewels Apr 17, 2026
8a582c8
chore(simplify): tighten tie-shuffle comments
ewels Apr 17, 2026
ca458d4
chore(simplify): use std::hash::DefaultHasher directly
ewels Apr 17, 2026
4b5cc8b
chore(simplify): replace where-clause with impl Fn on shuffle_tied_pr…
ewels Apr 17, 2026
716a816
chore(simplify): drop dead rg_ids() call and redundant attrs gate
ewels Apr 17, 2026
f23e00d
chore(simplify): introduce primary_rg_id helper for writer callsites
ewels Apr 17, 2026
845398f
chore(simplify): rewrite parsed_rg_lines with Vec::split
ewels Apr 17, 2026
471518a
chore: remove dead SamWriter::write_unmapped
ewels Apr 17, 2026
1514169
chore: apply cargo fmt
ewels Apr 17, 2026
8dc4262
chore: apply cargo fmt
ewels Apr 17, 2026
baeea81
Merge branch 'main' into feat/run-rng-seed
Psy-Fer Apr 20, 2026
e67864d
Merge pull request #5 from ewels/feat/run-rng-seed
Psy-Fer Apr 20, 2026
038c23f
Merge branch 'main' into feat/sam-rg-line
Psy-Fer Apr 20, 2026
e306046
Fix merge conflict squashing } braket
Psy-Fer Apr 20, 2026
0763745
Merge pull request #6 from ewels/feat/sam-rg-line
Psy-Fer Apr 20, 2026
6bdf490
feat(quant): add TranscriptomeIndex built from GTF exon groups
ewels Apr 17, 2026
ae8b253
feat(quant): project genome alignments onto transcripts (align_to_tra…
ewels Apr 17, 2026
35e3582
feat(quant): filter modes + softclip extension for transcriptome SAM
ewels Apr 17, 2026
51ebe28
feat(params): --quantTranscriptomeSAMoutput + TranscriptomeSAM valida…
ewels Apr 17, 2026
7600a8c
feat(io/bam,lib): wire Aligned.toTranscriptome.out.bam pipeline
ewels Apr 17, 2026
6008336
test: integration test for --quantMode TranscriptomeSAM
ewels Apr 17, 2026
ab5523a
chore(simplify): drop dead Display + allow_single_end on QuantTranscr…
ewels Apr 17, 2026
505a30f
chore(simplify): share a single rc_encode helper in transcriptome bui…
ewels Apr 17, 2026
557de39
chore(simplify): emit PE transcriptome records with one build call pe…
ewels Apr 17, 2026
eee8518
chore(simplify): share primary-hit + MAPQ picker between SE and PE
ewels Apr 17, 2026
724103f
chore(simplify): share BGZF writer setup between BamWriter constructors
ewels Apr 17, 2026
5781129
chore(simplify): collapse locals in extend_softclips trailing fixup
ewels Apr 17, 2026
c86c07d
chore(simplify): tighten filter_and_project docs + drop unread read_s…
ewels Apr 17, 2026
95bef01
chore(simplify): fix stale mate_or_junction_before comment in align_t…
ewels Apr 17, 2026
2e95a44
chore(simplify): drop speculative BamWriter::header accessor
ewels Apr 17, 2026
9725513
chore(simplify): accept IntoIterator in build_transcriptome_records_pe
ewels Apr 17, 2026
a31fc4f
chore(simplify): drop redundant StdHashMap alias in transcriptome tests
ewels Apr 17, 2026
a8686df
chore: apply cargo fmt
ewels Apr 21, 2026
982b96e
feat(quant): add tr_exi cumulative exon offset to TranscriptomeIndex
ewels Apr 22, 2026
a2a9bd0
feat(quant): add gene interning (gene_ids/names/biotypes + tr_gene_idx)
ewels Apr 22, 2026
5a38ea3
fix(quant): compute tr_exi in STAR's sorted order, not insertion order
ewels Apr 22, 2026
b259c23
feat(quant): write transcriptInfo.tab in STAR's exact byte format
ewels Apr 22, 2026
b735628
feat(quant): write exonInfo.tab in STAR's exact byte format
ewels Apr 22, 2026
69ee062
feat(quant): write geneInfo.tab in STAR's exact byte format
ewels Apr 22, 2026
dc5d45b
feat(quant): write exonGeTrInfo.tab in STAR's exact byte format
ewels Apr 22, 2026
6898536
feat(quant): write sjdbList.fromGTF.out.tab in STAR's exact byte format
ewels Apr 22, 2026
3c828d5
feat(quant): load TranscriptomeIndex from on-disk STAR files
ewels Apr 22, 2026
1349196
feat: persist transcriptome index at genomeGenerate, load at alignReads
ewels Apr 22, 2026
e6eed98
feat(align): add i_frag mate index to Exon
ewels Apr 22, 2026
bff2f8c
feat(quant): handle mate boundary in transcriptome projection
ewels Apr 22, 2026
7db1d40
feat(align): add PairedAlignment::combined_transcript_for_projection
ewels Apr 22, 2026
6351a68
test: verify byte-format parity of all 5 STAR-compatible index files
ewels Apr 22, 2026
0535f9d
fix(quant): match STAR's geneInfo.tab fallback strings
ewels Apr 22, 2026
fa29f13
test: add diff_star_transcriptome.sh — byte-for-byte parity script
ewels Apr 22, 2026
c6e1ea1
fix(genome): match STAR's genomeParameters.txt byte-for-byte
ewels Apr 22, 2026
96d071c
chore(simplify): reuse Genome::position_to_chr in TranscriptomeIndex …
ewels Apr 22, 2026
cbe4e39
chore(simplify): lift GTF attribute names + MissingGeneType to constants
ewels Apr 22, 2026
277415d
test: simplify diff script with a symlink pointing to per-tool index dir
ewels Apr 22, 2026
2b1b342
chore(simplify): drop redundant tr_gene_id string field from Transcri…
ewels Apr 22, 2026
304a39c
fix(params): don't require --sjdbGTFfile at alignReads when the index…
ewels Apr 22, 2026
649fd6e
fix(io/bam): write header with a lenient validator (STAR tRNA names)
ewels Apr 22, 2026
45792dd
Merge upstream/dev into feat/transcriptome-sam
ewels Apr 22, 2026
a26d636
chore(simplify): collapse try_pair_transcripts now that all callers s…
ewels Apr 22, 2026
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79 changes: 78 additions & 1 deletion Cargo.lock

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

1 change: 1 addition & 0 deletions Cargo.toml
Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@ flate2 = "1"
rayon = "1"
dashmap = "6"
chrono = "0.4"
rand = "0.8"

[dev-dependencies]
tempfile = "3"
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