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r1230: make juncevla work for paired-end SAM

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Heng Li
2025-03-29 22:43:44 -04:00
parent 618d33515e
commit e18935fbad
1 changed files with 5 additions and 1 deletions
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misc/paftools.js
+5 -1
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@@ -1,6 +1,6 @@
#!/usr/bin/env k8
var paftools_version = '2.28-r1209';
var paftools_version = '2.28-r1230-dirty';
/*****************************
***** Library functions *****
@@ -2494,6 +2494,10 @@ function paf_junceval(args)
} else { // SAM
ctg_name = t[2], pos = parseInt(t[3]) - 1, cigar = t[5];
var flag = parseInt(t[1]);
if (flag & 1) {
if (flag & 0x40) qname += '/1';
else if (flag & 0x80) qname += '/2';
}
if (flag&0x100) continue; // secondary
}