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r1197: sam2paf to output primary only

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This commit is contained in:
Heng Li
2024-03-19 21:47:31 -04:00
parent acab05781e
commit c7433c2811
1 changed files with 6 additions and 3 deletions
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9
misc/paftools.js
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@@ -1,6 +1,6 @@
#!/usr/bin/env k8
var paftools_version = '2.27-r1194-dirty';
var paftools_version = '2.27-r1197-dirty';
/*****************************
***** Library functions *****
@@ -1740,15 +1740,17 @@ function paf_gff2bed(args)
function paf_sam2paf(args)
{
var c, pri_only = false, long_cs = false;
while ((c = getopt(args, "pL")) != null) {
var c, pri_only = false, long_cs = false, pri_pri_only = false;
while ((c = getopt(args, "pPL")) != null) {
if (c == 'p') pri_only = true;
else if (c == 'P') pri_pri_only = pri_only = true;
else if (c == 'L') long_cs = true;
}
if (args.length == getopt.ind) {
print("Usage: paftools.js sam2paf [options] <in.sam>");
print("Options:");
print(" -p convert primary or supplementary alignments only");
print(" -P convert primary alignments only");
print(" -L output the cs tag in the long form");
exit(1);
}
@@ -1775,6 +1777,7 @@ function paf_sam2paf(args)
throw Error("at line " + lineno + ": inconsistent SEQ and QUAL lengths - " + t[9].length + " != " + t[10].length);
if (t[2] == '*' || (flag&4) || t[5] == '*') continue;
if (pri_only && (flag&0x100)) continue;
if (pri_pri_only && (flag&0x900)) continue;
var tlen = ctg_len[t[2]];
if (tlen == null) throw Error("at line " + lineno + ": can't find the length of contig " + t[2]);
// find tags