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output #mismatches/#dels/#ins in view

This commit is contained in:
Heng Li 2021-07-18 15:13:40 -04:00
parent 2546999639
commit 15118dd521
1 changed files with 7 additions and 1 deletions
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8
misc/paftools.js
View File

@ -1475,8 +1475,14 @@ function paf_view(args)
warn("WARNING: converting to BLAST-like alignment requires the 'cs' tag, which is absent on line " + lineno); warn("WARNING: converting to BLAST-like alignment requires the 'cs' tag, which is absent on line " + lineno);
continue; continue;
} }
var n_mm = 0, n_oi = 0, n_od = 0, n_ei = 0, n_ed = 0;
while ((m = re_cs.exec(cs)) != null) {
if (m[1] == '*') ++n_mm;
else if (m[1] == '+') ++n_oi, n_ei += m[2].length;
else if (m[1] == '-') ++n_od, n_ed += m[2].length;
}
line = line.replace(/\tc[sg]:Z:\S+/g, ""); // get rid of cs or cg tags line = line.replace(/\tc[sg]:Z:\S+/g, ""); // get rid of cs or cg tags
print('>' + line); print('>' + line + "\tmm:i:"+n_mm + "\toi:i:"+n_oi + "\tei:i:"+n_ei + "\tod:i:"+n_od + "\ted:i:"+n_ed);
var rs = parseInt(t[7]), qs = t[4] == '+'? parseInt(t[2]) : parseInt(t[3]); var rs = parseInt(t[7]), qs = t[4] == '+'? parseInt(t[2]) : parseInt(t[3]);
var n_blocks = 0; var n_blocks = 0;
while ((m = re_cs.exec(cs)) != null) { while ((m = re_cs.exec(cs)) != null) {