fix(stats): route no-seeds-no-clusters reads to UnmappedReason::Other#49
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pinin4fjords wants to merge 1 commit into
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fix(stats): route no-seeds-no-clusters reads to UnmappedReason::Other#49pinin4fjords wants to merge 1 commit into
UnmappedReason::Other#49pinin4fjords wants to merge 1 commit into
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The UnmappedReason enum had all four STAR-compatible variants (Other, TooShort, TooManyMismatches, TooManyLoci), but reads that failed before any transcript was generated were being recorded as TooShort. Log.final.out's "Reads unmapped: other" therefore always read 0 even when STAR would have classified the read in that bucket, inflating "too short" by the same count. Fix the routing at the no-seeds / no-clusters call site so reads without alignments are recorded as Other. Totals are unchanged; only the bucketing changes. Fixes scverse#48 Co-Authored-By: Claude <noreply@anthropic.com>
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Verified end-to-end with paired STAR + rustar runs on the same yeast PE inputs ( Unmapped buckets in
LGTM. |
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Summary
Log.final.outreportsNumber of reads unmapped: too shortandNumber of reads unmapped: otherusing STAR's exact field labels, but rustar was folding everything intotoo shortand always reportingother = 0. Reads that failed before a transcript was generated (no seeds / no clusters) were being misclassified astoo short, inflating that bar and zeroing out STAR'sotherbucket.On
WT_REP2pre-fix:too short = 4 193 (8.46 %),other = 0 (0 %)vs STAR's1 540 (3.11 %)and2 656 (5.36 %).Fix
Audit the
record_unmapped_reason(...)call sites and route the no-seeds / no-clusters path toUnmappedReason::Otherinstead ofUnmappedReason::TooShort. Totals unchanged; only the bucketing changes.Test plan
unmapped_other > 0and totals conservedother = 0updatedcargo buildcargo clippy --lib -- -D warningscargo fmt --checkFixes #48