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don't process hard clipped SEQ 

The full read sequence has to be present.
This commit is contained in:
Heng Li 2014-08-07 10:36:28 -04:00
parent 705aa53894
commit 5e56bec0f4
1 changed files with 11 additions and 2 deletions
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13
bwa-helper.js
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@ -468,6 +468,7 @@ function bwa_genalt(args)
h.rev = (s[1].charAt(0) == '-');
h.cigar = s[2];
h.NM = parseInt(s[3]);
h.hard = false;
var m, l_ins, n_ins, l_del, n_del, l_match, l_skip, l_clip;
l_ins = l_del = n_ins = n_del = l_match = l_skip = l_clip = 0;
while ((m = re_cigar.exec(h.cigar)) != null) {
@ -476,7 +477,10 @@ function bwa_genalt(args)
else if (m[2] == 'D') ++n_del, l_del += l;
else if (m[2] == 'I') ++n_ins, l_ins += l;
else if (m[2] == 'N') l_skip += l;
else if (m[2] == 'H' || m[2] == 'S') l_clip += l;
else if (m[2] == 'H' || m[2] == 'S') {
l_clip += l;
if (m[2] == 'H') h.hard = true;
}
}
h.end = h.start + l_match + l_del + l_skip;
h.NM = h.NM > l_del + l_ins? h.NM : l_del + l_ins;
@ -541,7 +545,12 @@ function bwa_genalt(args)
var NM = (m = /\tNM:i:(\d+)/.exec(line)) == null? '0' : m[1];
var t = line.split("\t");
var flag = parseInt(t[1]);
hits.push(parse_hit([t[2], ((flag&16)?'-':'+') + t[3], t[5], NM], opt));
var h = parse_hit([t[2], ((flag&16)?'-':'+') + t[3], t[5], NM], opt);
if (h.hard) { // the following does not work with hard clipped SEQ
print(line);
continue;
}
hits.push(h);
for (var i = 0; i < XA_strs.length; ++i) // hits in the XA tag
if (XA_strs[i] != '') // as the last symbol in an XA tag is ";", the last split is an empty string
hits.push(parse_hit(XA_strs[i].split(","), opt));