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expose mapQ threshold to command line of pafcmp

This commit is contained in:
Heng Li 2021-08-06 19:41:46 -04:00
parent 70393eb46e
commit f7271a7c24
1 changed files with 5 additions and 2 deletions
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7
misc/paftools.js
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@ -2949,13 +2949,16 @@ function paf_vcfsel(args)
function paf_pafcmp(args)
{
var c, opt = { min_len:5000, min_mapq:5, min_ovlp:0.5 };
while ((c = getopt(args, "c:")) != null) {
var c, opt = { min_len:5000, min_mapq:10, min_ovlp:0.5 };
while ((c = getopt(args, "q:")) != null) {
if (c == 'q') opt.min_mapq = parseInt(opt.arg);
}
var buf = new Bytes();
if (args.length - getopt.ind < 2) {
print("Usage: paftools.js pafcmp [options] <base.paf> <test.paf>");
print("Options:");
print(" -q INT min mapping quality [" + opt.min_mapq + "]");
return 1;
}