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Report per-aln stats as per-aligned, ignoring unmapped reads #4921

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Report per-aln stats as per-aligned, ignoring unmapped reads #4921

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a00bc1c
Report per-aln stats as per-aligned, ignoring unmapped reads
faithokamoto Jun 5, 2026
22127ce
fix denom text
faithokamoto Jun 5, 2026
81ba66e
update expected output
faithokamoto Jun 5, 2026
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4 changes: 2 additions & 2 deletions src/subcommand/stats_main.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -1119,13 +1119,13 @@ int main_stats(int argc, char** argv) {
}
cout << "Matches: " << combined.total_matched_bases << " bp";
if (combined.total_alignments > 0) {
cout << " (" << combined.total_matched_bases / static_cast<double>(combined.total_alignments) << " bp/alignment)";
cout << " (" << combined.total_matched_bases / static_cast<double>(combined.total_aligned) << " bp/aligned)";
}
cout << endl;
cout << "Softclips: " << combined.total_softclipped_bases << " bp";
if (combined.total_alignments > 0) {
cout << " (" << 100 * combined.total_softclipped_bases / static_cast<double>(combined.total_bases) << "% of bases, "
<< combined.total_softclipped_bases / static_cast<double>(combined.total_alignments) << " bp/alignment)";
<< combined.total_softclipped_bases / static_cast<double>(combined.total_aligned) << " bp/aligned)";
}
cout << " in " << combined.total_softclips << " read events" << endl;
if(verbose) {
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4 changes: 2 additions & 2 deletions test/correct/10_vg_stats/15.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -11,8 +11,8 @@ Mapping quality: mean 60, median 60, stdev 0, max 60 (100 reads)
Insertions: 0 bp in 0 read events
Deletions: 0 bp in 0 read events
Substitutions: 0 bp in 0 read events
Matches: 10000 bp (100 bp/alignment)
Softclips: 0 bp (0% of bases, 0 bp/alignment) in 0 read events
Matches: 10000 bp (100 bp/aligned)
Softclips: 0 bp (0% of bases, 0 bp/aligned) in 0 read events
Unvisited nodes: 4/208 (4 bp)
Single-visited nodes: 11/208 (18 bp)
Significantly biased heterozygous sites: 2/62 (3.22581%)
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