Add mean_zero_coverage_length coverage method#292
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Add a new coverage method, mean_zero_coverage_length, that reports the average length (in base pairs) of the regions of each contig or genome that have zero coverage. Within a covered contig, each maximal run of consecutive zero-coverage bases is one region. An entirely-unobserved contig (or, in genome mode, an entry with no reads mapped at all) is treated as a single zero-coverage region spanning its whole length, which keeps results identical regardless of whether the streaming (print_zero_coverage) or non-streaming (calculate_coverage) code path is taken. A contig/genome with no zero-coverage positions is reported as 0. Like the other structural estimators (length, count, reads_per_base, anir), this method does not compute a covered fraction and so cannot be combined with --min-covered-fraction > 0. Includes unit tests for the estimator logic, an end-to-end contig test, a cmdline integration test, and README/help documentation.
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| if *num_mapped_reads == 0 { | ||
| // No reads mapped to this entry at all, so the whole entry is | ||
| // a single zero-coverage region spanning its full length. | ||
| // Reporting the total length here (rather than the per-contig | ||
| // average) keeps results identical to the print_zero_coverage | ||
| // path, which only knows the entry's total length. | ||
| return unobserved_bases as f32; |
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In genome mode with --no-zeros, src/genome.rs decides whether to print an entry by checking whether any calculated coverage is > 0; returning the entry length here when num_mapped_reads == 0 makes completely unmapped genomes look nonzero for -m mean_zero_coverage_length, so coverm genome --no-zeros -m mean_zero_coverage_length will still emit genomes with zero read coverage. This needs a separate path for reporting the length without using that positive value as the print/no-print signal.
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Summary
Adds a new coverage method,
mean_zero_coverage_length, that reports the average length (in base pairs) of the regions of each contig or genome that have zero coverage.This builds on top of #290 (the
coverm makedbbranch), so its diff is included here; this PR's own changes are the new coverage method.Behaviour
1000).0.Cross-path consistency
Genome coverage is computed via two code paths — streaming (
--separator) and non-streaming (--genome-fasta-files). For an entirely-unobserved multi-contig genome, the streaming path only knows the genome's total length (viaprint_zero_coverage). To keep results identical regardless of input format, an entry with zero mapped reads is defined as a single region of its full length. The estimator'snum_mapped_readsis available in bothcalculate_coverageandprint_zero_coverage, so both paths agree, and it also distinguishes an absent entry (→ length) from a fully-covered one (→ 0).Like the other structural estimators (
length,count,reads_per_base,anir), this method does not compute a covered fraction and so cannot be combined with--min-covered-fraction > 0(it errors with a clear message).Changes
src/mosdepth_genome_coverage_estimators.rs: newMeanZeroCoverageLengthEstimatorvariant, all trait arms, and 4 unit tests.src/bin/coverm.rs: method dispatch and--min-covered-fractionincompatibility guard.src/cli.rs: added to bothgenome/contigvalue-parser lists and both help tables.src/contig.rs: end-to-end test (coveredseq1→ 68.25, uncoveredseq2→ 1000).tests/test_cmdline.rs: cmdline integration test.README.md: row in the calculation-methods table.Testing
cargo clippy -- -D warningsandcargo fmt -- --checkare clean (enforced by the pre-commit hook).test_streaming_bam_file) fails in this environment only becausesamtools/bwaare not installed.The generated
docs/coverm-*.htmlman pages were not regenerated, as that requires theman/pandoctooling used at release time; the source README and CLI help text are updated.https://claude.ai/code/session_0126FFDNupzAHRS5m74JA9Zp
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