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print cov-1 regions (not BED output any more)

This commit is contained in:
Heng Li 2017-11-12 18:45:49 -05:00
parent 8c8d446820
commit 03169d590b
1 changed files with 15 additions and 6 deletions
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21
misc/paf2diff.js
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@ -96,25 +96,31 @@ while (file.readline(buf) >= 0) {
var ctg = t[5], x = t[7], end = t[8];
// compute regions covered by 1 contig
if (ctg != c1_ctg || x >= c1_end) {
if (c1_counted)
if (c1_counted && c1_end > c1_start) {
c1_len += c1_end - c1_start;
print('R', c1_ctg, c1_start, c1_end);
}
c1_ctg = ctg, c1_start = x, c1_end = end;
c1_counted = (t[10] >= min_var_len);
} else if (end > c1_end) { // overlap
if (c1_counted && x > c1_start)
if (c1_counted && x > c1_start) {
c1_len += x - c1_start;
print('R', c1_ctg, c1_start, x);
}
c1_start = c1_end, c1_end = end;
c1_counted = (t[10] >= min_var_len);
} else { // contained
if (c1_counted && x > c1_start)
if (c1_counted && x > c1_start) {
c1_len += x - c1_start;
print('R', c1_ctg, c1_start, x);
}
c1_start = end;
}
// output variants ahead of this alignment
while (out.length) {
if (out[0][0] != ctg || out[0][2] <= x) {
count_var(out[0]);
print(out[0].join("\t"));
print('V', out[0].join("\t"));
out.shift();
} else break;
}
@ -156,10 +162,13 @@ while (file.readline(buf) >= 0) {
}
a.push([t[5], t[7], t[8]]);
}
if (c1_counted) c1_len += c1_end - c1_start;
if (c1_counted && c1_end > c1_start) {
c1_len += c1_end - c1_start;
print('R', c1_ctg, c1_start, c1_end);
}
while (out.length) {
count_var(out[0]);
print(out[0].join("\t"));
print('V', out[0].join("\t"));
out.shift();
}