feat(reads): raw FASTQ quality control - #160

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BenjaminDEMAILLE wants to merge 25 commits into

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BenjaminDEMAILLE:feat/reads-fastq

Commits on Aug 28, 2026

refactor: move bam_flags, cpp_rng and preseq into src/common/

BenjaminDEMAILLE
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claude
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2f57c13
refactor: move bam_stat and the samtools writers into src/common/

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f4721a2
refactor: lift BamStatAccum into src/common/bam_stat_accum.rs

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6d57f5f
docs: describe the src/common module split

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c3f8c64
test: guard the rna re-export shims against silent breakage

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701ea6d
test: add the DNA test dataset and its reference outputs

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8a9ab64
feat(cli): add the dna subcommand surface

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d72dcf2
feat(config): add the dna configuration section

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9db53ea
feat(dna): add the per-contig depth accumulator

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7143c6d
feat(dna): correct mate overlaps in the depth engine

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e64cfd9
feat(dna): add the mosdepth-compatible output writers

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726bfbf
feat(dna): wire up the run_dna pipeline

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11190bb
feat(dna): add the DNA JSON summary block and citations

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4198359
docs: describe the dna subcommand in AGENTS.md and the changelog

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10e711a
feat(dna): write the .csi companion indexes, cite the samtools version used

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38abe05
feat(dna): reimplement Picard CollectInsertSizeMetrics

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d4a0cc2
feat(dna): reimplement Picard CollectWgsMetrics

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42263a0
feat(dna): reimplement Picard CollectGcBiasMetrics

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9cf0784
feat(dna): add targeted mode and Picard CollectHsMetrics

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d5d4d89
docs: add the DNA pages and the dna CLI reference

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a96e30c
feat(dna): reimplement Qualimap bamqc

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fc1a045
feat(protein): add the protein subcommand and its sequence mode

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907b328

Commits on Aug 29, 2026

fix(protein): N50_num counts distinct lengths, not sequences

BenjaminDEMAILLE
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claude
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a5a19c6
feat(protein): add the spectra mode for mass spectrometry QC

BenjaminDEMAILLE
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claude
committed
347c8ee
feat(reads): add raw FASTQ quality control

BenjaminDEMAILLE
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claude
committed
5773060

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feat(reads): raw FASTQ quality control - #160

feat(reads): raw FASTQ quality control#160
BenjaminDEMAILLE wants to merge 25 commits into
seqeralabs:mainfrom
BenjaminDEMAILLE:feat/reads-fastq

Commits on Aug 28, 2026

refactor: move bam_flags, cpp_rng and preseq into src/common/

refactor: move bam_stat and the samtools writers into src/common/

refactor: lift BamStatAccum into src/common/bam_stat_accum.rs

docs: describe the src/common module split

test: guard the rna re-export shims against silent breakage

test: add the DNA test dataset and its reference outputs

feat(cli): add the dna subcommand surface

feat(config): add the dna configuration section

feat(dna): add the per-contig depth accumulator

feat(dna): correct mate overlaps in the depth engine

feat(dna): add the mosdepth-compatible output writers

feat(dna): wire up the run_dna pipeline

feat(dna): add the DNA JSON summary block and citations

docs: describe the dna subcommand in AGENTS.md and the changelog

feat(dna): write the .csi companion indexes, cite the samtools version used

feat(dna): reimplement Picard CollectInsertSizeMetrics

feat(dna): reimplement Picard CollectWgsMetrics

feat(dna): reimplement Picard CollectGcBiasMetrics

feat(dna): add targeted mode and Picard CollectHsMetrics

docs: add the DNA pages and the dna CLI reference

feat(dna): reimplement Qualimap bamqc

feat(protein): add the protein subcommand and its sequence mode

Commits on Aug 29, 2026

fix(protein): N50_num counts distinct lengths, not sequences

feat(protein): add the spectra mode for mass spectrometry QC

feat(reads): add raw FASTQ quality control