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make calling work with sam2paf output

This commit is contained in:
Heng Li 2018-03-02 10:03:06 -05:00
parent 2bfdad34bb
commit 1770988627
1 changed files with 13 additions and 5 deletions
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18
misc/paftools.js
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@ -346,7 +346,7 @@ function paf_call(args)
else ++n_del[3];
} else {
++n_sub[0];
var s = o[5] + o[6];
var s = (o[5] + o[6]).toLowerCase();
if (s == 'ag' || s == 'ga' || s == 'ct' || s == 'tc')
++n_sub[1];
else ++n_sub[2];
@ -357,8 +357,7 @@ function paf_call(args)
var c1_ctg = null, c1_start = 0, c1_end = 0, c1_counted = false, c1_len = 0;
while (file.readline(buf) >= 0) {
var line = buf.toString();
if (!/\ts2:i:/.test(line)) continue; // skip secondary alignments
var m, t = line.split("\t", 12);
var m, t = line.split("\t");
for (var i = 6; i <= 11; ++i)
t[i] = parseInt(t[i]);
if (t[10] < min_cov_len || t[11] < min_mapq) continue;
@ -367,6 +366,16 @@ function paf_call(args)
t[i] = parseInt(t[i]);
var ctg = t[5], x = t[7], end = t[8];
var query = t[0], rev = (t[4] == '-'), y = rev? t[3] : t[2];
// collect tags
var cs = null, tp = null, have_s1 = false, have_s2 = false;
for (var i = 12; i < t.length; ++i) {
if (t[i].substr(0, 5) == 'cs:Z:') cs = t[i].substr(5);
else if (t[i].substr(0, 5) == 'tp:A:') tp = t[i][5];
else if (t[i].substr(0, 5) == 's1:i:') have_s1 = true;
else if (t[i].substr(0, 5) == 's2:i:') have_s2 = true;
}
if (have_s1 && !have_s2) continue;
if (tp != null && (tp == 'S' || tp == 'i')) continue;
// compute regions covered by 1 contig
if (ctg != c1_ctg || x >= c1_end) {
if (c1_counted && c1_end > c1_start) {
@ -409,8 +418,7 @@ function paf_call(args)
a.length = k;
// core loop
if (t[10] >= min_var_len) {
if ((m = /\tcs:Z:(\S+)/.exec(line)) == null) continue; // no cs tag
var cs = m[1];
if (cs == null) continue; // no cs tag
var blen = 0, n_diff = 0;
tot_len += t[10];
while ((m = re_cs.exec(cs)) != null) {