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r1194: output NM in sam2paf

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Heng Li
2024-03-19 09:55:16 -04:00
parent b6762503a9
commit 98c23bc6d2
1 changed files with 5 additions and 2 deletions
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misc/paftools.js
+5 -2
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@@ -1,6 +1,6 @@
#!/usr/bin/env k8 #!/usr/bin/env k8
var paftools_version = '2.27-r1193'; var paftools_version = '2.27-r1194-dirty';
/***************************** /*****************************
***** Library functions ***** ***** Library functions *****
@@ -1887,7 +1887,10 @@ function paf_sam2paf(args)
// optional tags // optional tags
var type = flag&0x100? 'S' : 'P'; var type = flag&0x100? 'S' : 'P';
var tags = ["tp:A:" + type]; var tags = ["tp:A:" + type];
if (NM != null) tags.push("mm:i:"+mm); if (NM != null) {
tags.push("NM:i:"+NM);
tags.push("mm:i:"+mm);
}
tags.push("gn:i:"+(I[1]+D[1]), "go:i:"+(I[0]+D[0]), "cg:Z:" + t[5].replace(/\d+[SH]/g, '')); tags.push("gn:i:"+(I[1]+D[1]), "go:i:"+(I[0]+D[0]), "cg:Z:" + t[5].replace(/\d+[SH]/g, ''));
if (cs_str != null) tags.push("cs:Z:" + cs_str); if (cs_str != null) tags.push("cs:Z:" + cs_str);
else if (cs.length > 0) tags.push("cs:Z:" + cs.join("")); else if (cs.length > 0) tags.push("cs:Z:" + cs.join(""));