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faster tag parsing

This commit is contained in:
Heng Li 2018-03-02 10:09:14 -05:00
parent 1770988627
commit 9aea79d621
1 changed files with 7 additions and 6 deletions
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13
misc/paftools.js
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@ -353,11 +353,12 @@ function paf_call(args)
}
}
var re_tags = /\t([A-Za-z]{2}:[AZif]):(\S+)/g;
var a = [], out = [];
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();
var m, t = line.split("\t");
var m, t = line.split("\t", 12);
for (var i = 6; i <= 11; ++i)
t[i] = parseInt(t[i]);
if (t[10] < min_cov_len || t[11] < min_mapq) continue;
@ -368,11 +369,11 @@ function paf_call(args)
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;
while ((m = re_tags.exec(line)) != null) {
if (m[1] == 'cs:Z') cs = m[2];
else if (m[1] == 'tp:A') tp = m[2];
else if (m[1] == 's1:i') have_s1 = true;
else if (m[1] == 's2:i') have_s2 = true;
}
if (have_s1 && !have_s2) continue;
if (tp != null && (tp == 'S' || tp == 'i')) continue;