feat: add seq-content command and seq-stats improvements - #28
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seq-content counts canonical k-mers per bed region category. seq-stats gains numpy-style quantiles, FIFO input support, and better filters. Rebased flat onto the rust-htslib 1.0 migration: the faidx free workaround is gone because fetch_seq now returns an owned Vec.
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Adds the
rb seq-contentcommand. It counts canonical k-mers (k 1-7) in bed regions, grouped by the region name column, and prints one row per group with one column per canonical k-mer.Also improves
rb seq-stats: numpy-style linear-interpolation quantiles, clean one-decimal quantile headers, FIFO and process-substitution inputs, and skipping only missing or empty regular files.Review status: a multi-agent review ran on this branch earlier. The confirmed findings are fixed in this tree: per-region fasta fetches instead of one whole-chromosome buffer per contig, k=0 rejected at the CLI, and the input prefilter keeps FIFOs.
Note on the rebase: the branch history was flattened onto main after the rust-htslib 1.0 migration. The earlier faidx free workaround is removed, because
fetch_seqnow returns an owned Vec and freeing its pointer would be a double free.