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require overlap ratio when considering centromere

This commit is contained in:
Heng Li 2021-03-11 19:11:44 -05:00
parent 1c4b7e8a48
commit 1b0bb7b0ba
1 changed files with 15 additions and 6 deletions
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21
misc/paftools.js
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@ -2604,12 +2604,13 @@ function paf_parseNum(s) {
function paf_misjoin(args)
{
var c, min_seg_len = 1000000, max_gap = 1000000, fn_cen = null, show_long = false, show_err = false;
var c, min_seg_len = 1000000, max_gap = 1000000, fn_cen = null, show_long = false, show_err = false, cen_ratio = 0.5;
var n_diff = [0, 0], n_gap = [0, 0], n_inv = [0, 0], n_inv_end = [0, 0];
while ((c = getopt(args, "l:g:c:pe")) != null) {
while ((c = getopt(args, "l:g:c:per:")) != null) {
if (c == 'l') min_seg_len = paf_parseNum(getopt.arg);
else if (c == 'g') max_gap = paf_parseNum(getopt.arg);
else if (c == 'c') fn_cen = getopt.arg;
else if (c == 'r') cen_ratio = parseFloat(getopt.arg);
else if (c == 'p') show_long = true;
else if (c == 'e') show_err = true;
}
@ -2617,6 +2618,7 @@ function paf_misjoin(args)
print("Usage: paftools.js misjoin [options] <in.paf>");
print("Options:");
print(" -c FILE BED for centromeres []");
print(" -r FLOAT count a centromeric event if overlap ratio > FLOAT [" + cen_ratio + "]");
print(" -l NUM min alignment block length [1m]");
print(" -g NUM max gap size [1m]");
print(" -e output misjoins not involving centromeres");
@ -2636,12 +2638,15 @@ function paf_misjoin(args)
}
function test_cen(cen, chr, st, en) {
var b = cen[chr];
var b = cen[chr], len = 0;
if (b == null) return false;
for (var j = 0; j < b.length; ++j)
if (b[j][0] < en && b[j][1] > st)
return true;
return false;
if (b[j][0] < en && b[j][1] > st) {
var s = b[j][0] > st? b[j][0] : st;
var e = b[j][1] < en? b[j][1] : en;
len += e - s;
}
return len < (en - st) * cen_ratio? false : true;
}
function process(a) {
@ -2672,6 +2677,10 @@ function paf_misjoin(args)
var gap = dr > dq? dr - dq : dq - dr;
if (gap > max_gap) {
if (ov[0] || ov[1]) ++n_gap[1];
else if (show_err) {
print("G", a[i-1].slice(0, 12).join("\t"));
print("G", a[i].slice(0, 12).join("\t"));
}
++n_gap[0];
}
} else if (i + 1 < a.length && a[i+1][4] == a[i-1][4]) { // bracketed inversion