perf(concat): block-copy concatenation instead of SeqRecord round-trip (89x faster, -2.6 GB) - #5

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sanjaynagi-eit wants to merge 14 commits into

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perf/concat-and-fasta-io

Commits on Aug 13, 2026

perf(concat): concatenate reads and contigs by block copy, not SeqRecords
sanjaynagi-eit
committed
1147f80
perf(qc): compress chopper output with bgzip, and wait on every stage
sanjaynagi-eit
committed
53f72f0
test: repair the truncated input_half.fastq.gz fixture
sanjaynagi-eit
committed
fa70e82

Commits on Aug 18, 2026

fix: restore 75bp long read cropping ignored by chopper >=0.11.0

gbouras13
and
claude
committed
0148dc8
test: restore the concat.fastq fixture deleted in 53f72f0

gbouras13
and
claude
committed
4599cbc
fix(qc): reap killed stages on the chopper error path

gbouras13
and
claude
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162ad5a
Merge branch 'fix/chopper-fixed-crop' into claude/blissful-burnell-fc1477
gbouras13
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aabce74
fix(qc): make chopper failures fatal instead of silently empty

gbouras13
and
claude
committed
51b4761

Commits on Aug 24, 2026

docs: credit #88 in the 1.8.4 release notes

gbouras13
and
claude
committed
c448a07

Commits on Sep 4, 2026

Merge pull request #89 from gbouras13/pr88-review-fixes
gbouras13
authored
515e105

Commits on Sep 7, 2026

Merge remote-tracking branch 'origin/main' into pr90-push
gbouras13
committed
2ed3216
fix(concat): write concatenated output atomically

gbouras13
and
claude
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bf0e616
fix(plass_class): keep an empty chromosome.fasta fatal

gbouras13
and
claude
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bc1d8b6
chore: release 1.8.5

gbouras13
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claude
committed
236a5f5