zzh
/
bwa
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

keep RG

This commit is contained in:
Heng Li 2014-10-27 10:45:07 -04:00
parent dbe74ca9b8
commit 5c87869d91
1 changed files with 2 additions and 0 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

2
bwa-postalt.js
View File

@ -577,6 +577,7 @@ function bwa_postalt(args)
// stage the hits generated from the XA tag // stage the hits generated from the XA tag
var cnt = 0; var cnt = 0;
var rg = (m = /\t(RG:Z:\S+)/.exec(line)) != null? m[1] : null;
for (var i = 0; i < hits.length; ++i) { for (var i = 0; i < hits.length; ++i) {
if (opt.verbose >= 5) print(obj2str(hits[i])); if (opt.verbose >= 5) print(obj2str(hits[i]));
if (hits[i].g != reported_g || i == reported_i) continue; if (hits[i].g != reported_g || i == reported_i) continue;
@ -592,6 +593,7 @@ function bwa_postalt(args)
} }
s.push("NM:i:" + hits[i].NM); s.push("NM:i:" + hits[i].NM);
if (hits[i].lifted_str) s.push("lt:Z:" + hits[i].lifted_str); if (hits[i].lifted_str) s.push("lt:Z:" + hits[i].lifted_str);
if (rg != null) s.push(rg);
buf2.push(s); buf2.push(s);
} }
} }