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work with targets in BED12

This commit is contained in:
Heng Li 2018-01-07 19:39:25 -05:00
parent bf72969ab1
commit 248b43cc47
1 changed files with 41 additions and 10 deletions
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51
misc/cnt-feat.js
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@ -66,6 +66,17 @@ Interval.merge = function(a, sorted)
a.length = k + 1;
}
Interval.dedup = function(a, sorted)
{
if (typeof sorted == 'undefined') sorted = true;
if (!sorted) Interval.sort(a);
var k = 0;
for (var i = 1; i < a.length; ++i)
if (a[k][0] != a[i][0] || a[k][1] != a[i][1])
a[++k] = a[i].slice(0);
a.length = k + 1;
}
Interval.index_end = function(a, sorted)
{
if (a.length == 0) return;
@ -125,13 +136,14 @@ Interval.find_ovlp = function(a, st, en)
function main(args)
{
var c, print_len = false;
while ((c = getopt(args, "l")) != null) {
if (c == 'l') print_len = true;
var c, print_len = false, to_merge = true, to_dedup = false;
while ((c = getopt(args, "pd")) != null) {
if (c == 'p') print_len = true;
else if (c == 'd') to_dedup = true, to_merge = false;
}
if (args.length - getopt.ind < 2) {
print("Usage: k8 cnt-feat.js <target.bed> <feature.bed>");
print("Usage: k8 cnt-feat.js [options] <target.bed> <feature.bed>");
exit(1);
}
@ -143,13 +155,32 @@ function main(args)
var t = buf.toString().split("\t");
if (target[t[0]] == null)
target[t[0]] = [];
target[t[0]].push([parseInt(t[1]), parseInt(t[2]), 0, 0, 0]);
var bst = parseInt(t[1]);
var ben = parseInt(t[2]);
if (t.length >= 12 && /^\d+$/.test(t[9])) {
t[9] = parseInt(t[9]);
var sz = t[10].split(",");
var st = t[11].split(",");
for (var i = 0; i < t[9]; ++i) {
st[i] = parseInt(st[i]);
sz[i] = parseInt(sz[i]);
target[t[0]].push([bst + st[i], bst + st[i] + sz[i], 0, 0, 0]);
}
} else {
target[t[0]].push([bst, ben, 0, 0, 0]);
}
}
file.close();
//warn('Read the target BED');
for (var chr in target)
Interval.index_end(target[chr], false);
//warn('Indexed the target BED');
var n_target_intv = 0;
for (var chr in target) {
if (to_merge) Interval.merge(target[chr], false);
else if (to_dedup) Interval.dedup(target[chr], false);
else Interval.sort(target[chr]);
n_target_intv += target[chr].length;
Interval.index_end(target[chr]);
}
warn("# target intervals: " + n_target_intv);
var tot_len = 0, hit_len = 0;
file = new File(args[getopt.ind+1]);
@ -198,7 +229,7 @@ function main(args)
feat_hit_len += en - st;
}
hit_len += feat_hit_len;
if (print_len) print(feat_len, feat_hit_len, buf);
if (print_len) print('F', t.slice(0, 4).join("\t"), feat_len, feat_hit_len);
}
file.close();