Add Scaffold N50 and Contig N50 to the assembly summary report - #6
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printSummary now reports Scaffold N50 (over path/scaffold sizes) and Contig N50 (over gap-split contig lengths), next to the existing Total gaps line. computeSummaryCounts accumulates per-path scaffold and contig lengths; a small computeN50() helper returns the standard N50. Adds scripts/test_n50.sh and a test-n50 make target validating both on a crafted two-scaffold, one-gap assembly.
The Scaffold N50 / Contig N50 additions to the assembly summary report change every report-bearing golden .tst. Regenerated via teloscope-generate-tests (make all); same command-hash filenames, only the two N50 lines added. val.sh now passes 227/0.
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Summary
Adds Scaffold N50 and Contig N50 to the per-assembly summary report (
*_report.tsv/ stdout), next to the existingTotal gapsline. This completes the structural-QC fields Teloscope already emits (gaps, scaffold length) so downstream analyses can read N50 straight from the freeze instead of a separate gfastats pass.Details
computeSummaryCounts()accumulates per-path scaffold lengths (pathData.pathSize) and contig lengths (path runs split atgapInfos).computeN50()helper returns the standard N50 (sort desc, length crossing 50% of total).gfalibssubmodule change.Report
Tests
scripts/test_n50.sh(+make test-n50): two-scaffold, one-gap assembly → asserts Scaffold N50 = 1650, Contig N50 = 800.make test-gapsregression: 12/12 pass.