From 92ec8bd8598eb90ad1e1a52e92fccfe19ae110aa Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 26 Sep 2017 12:04:35 -0400 Subject: [PATCH] added the /1 or /2 suffix --- misc/sam2paf.js | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/misc/sam2paf.js b/misc/sam2paf.js index 86d7c0e..e0bcd2e 100644 --- a/misc/sam2paf.js +++ b/misc/sam2paf.js @@ -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")); }