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added the /1 or /2 suffix

This commit is contained in:
Heng Li 2017-09-26 12:04:35 -04:00
parent 55d1e4f638
commit 92ec8bd859
1 changed files with 4 additions and 1 deletions
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5
misc/sam2paf.js
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@ -103,7 +103,10 @@ while (file.readline(buf) >= 0) {
if (flag&16) qs = clip[1], qe = qlen - clip[0];
else qs = clip[0], qe = qlen - clip[1];
var ts = parseInt(t[3]) - 1, te = ts + M + D[1] + N;
var a = [t[0], qlen, qs, qe, flag&16? '-' : '+', t[2], tlen, ts, te, match, blen, t[4]];
var qname = t[0];
if ((flag&1) && (flag&0x40)) qname += '/1';
if ((flag&1) && (flag&0x80)) qname += '/2';
var a = [qname, qlen, qs, qe, flag&16? '-' : '+', t[2], tlen, ts, te, match, blen, t[4]];
print(a.join("\t"), extra.join("\t"));
}