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feat(protein): mass spectrometry QC from mzML - #159

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BenjaminDEMAILLE wants to merge 24 commits into

seqeralabs:mainfrom

BenjaminDEMAILLE:feat/protein-spectra

Commits on Aug 28, 2026
- refactor: move bam_flags, cpp_rng and preseq into src/common/
  
  BenjaminDEMAILLE
  and
  claude
  committed
  2f57c13
- refactor: move bam_stat and the samtools writers into src/common/
  
  BenjaminDEMAILLE
  and
  claude
  committed
  f4721a2
- refactor: lift BamStatAccum into src/common/bam_stat_accum.rs
  
  BenjaminDEMAILLE
  and
  claude
  committed
  6d57f5f
- docs: describe the src/common module split
  
  BenjaminDEMAILLE
  and
  claude
  committed
  c3f8c64
- test: guard the rna re-export shims against silent breakage
  
  BenjaminDEMAILLE
  and
  claude
  committed
  701ea6d
- test: add the DNA test dataset and its reference outputs
  
  BenjaminDEMAILLE
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  claude
  committed
  8a9ab64
- feat(cli): add the dna subcommand surface
  
  BenjaminDEMAILLE
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  claude
  committed
  d72dcf2
- feat(config): add the dna configuration section
  
  BenjaminDEMAILLE
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  claude
  committed
  9db53ea
- feat(dna): add the per-contig depth accumulator
  
  BenjaminDEMAILLE
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  claude
  committed
  7143c6d
- feat(dna): correct mate overlaps in the depth engine
  
  BenjaminDEMAILLE
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  claude
  committed
  e64cfd9
- feat(dna): add the mosdepth-compatible output writers
  
  BenjaminDEMAILLE
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  claude
  committed
  726bfbf
- feat(dna): wire up the run_dna pipeline
  
  BenjaminDEMAILLE
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  claude
  committed
  11190bb
- feat(dna): add the DNA JSON summary block and citations
  
  BenjaminDEMAILLE
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  claude
  committed
  4198359
- docs: describe the dna subcommand in AGENTS.md and the changelog
  
  BenjaminDEMAILLE
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  claude
  committed
  10e711a
- feat(dna): write the .csi companion indexes, cite the samtools version used
  
  BenjaminDEMAILLE
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  claude
  committed
  38abe05
- feat(dna): reimplement Picard CollectInsertSizeMetrics
  
  BenjaminDEMAILLE
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  claude
  committed
  d4a0cc2
- feat(dna): reimplement Picard CollectWgsMetrics
  
  BenjaminDEMAILLE
  and
  claude
  committed
  42263a0
- feat(dna): reimplement Picard CollectGcBiasMetrics
  
  BenjaminDEMAILLE
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  claude
  committed
  9cf0784
- feat(dna): add targeted mode and Picard CollectHsMetrics
  
  BenjaminDEMAILLE
  and
  claude
  committed
  d5d4d89
- docs: add the DNA pages and the dna CLI reference
  
  BenjaminDEMAILLE
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  claude
  committed
  a96e30c
- feat(dna): reimplement Qualimap bamqc
  
  BenjaminDEMAILLE
  and
  claude
  committed
  fc1a045
- feat(protein): add the protein subcommand and its sequence mode
  
  BenjaminDEMAILLE
  and
  claude
  committed
  907b328
Commits on Aug 29, 2026
- fix(protein): N50_num counts distinct lengths, not sequences
  
  BenjaminDEMAILLE
  and
  claude
  committed
  a5a19c6
- feat(protein): add the spectra mode for mass spectrometry QC
  
  BenjaminDEMAILLE
  and
  claude
  committed
  347c8ee

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feat(protein): mass spectrometry QC from mzML - #159

feat(protein): mass spectrometry QC from mzML#159
BenjaminDEMAILLE wants to merge 24 commits into
seqeralabs:mainfrom
BenjaminDEMAILLE:feat/protein-spectra

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