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option to print errors only

This commit is contained in:
Heng Li 2021-02-07 12:58:03 -05:00
parent 75c8933511
commit 194b457e79
1 changed files with 13 additions and 2 deletions
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15
misc/paftools.js
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@ -2604,13 +2604,14 @@ function paf_parseNum(s) {
function paf_misjoin(args)
{
var c, min_seg_len = 1000000, max_gap = 1000000, fn_cen = null, show_long = false;
var c, min_seg_len = 1000000, max_gap = 1000000, fn_cen = null, show_long = false, show_err = false;
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:p")) != null) {
while ((c = getopt(args, "l:g:c:pe")) != 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 == 'p') show_long = true;
else if (c == 'e') show_err = true;
}
if (args.length == getopt.ind) {
print("Usage: paftools.js misjoin [options] <in.paf>");
@ -2618,6 +2619,7 @@ function paf_misjoin(args)
print(" -c FILE BED for centromeres []");
print(" -l NUM min alignment block length [1m]");
print(" -g NUM max gap size [1m]");
print(" -e output misjoins not involving centromeres");
print(" -p output long alignment blocks for debugging");
return;
}
@ -2659,6 +2661,10 @@ function paf_misjoin(args)
ov[1] = test_cen(cen, a[i][5], a[i][7], a[i][8]);
if (a[i-1][5] != a[i][5]) { // different chr
if (ov[0] || ov[1]) ++n_diff[1];
else if (show_err) {
print("J", a[i-1].slice(0, 12).join("\t"));
print("J", a[i].slice(0, 12).join("\t"));
}
++n_diff[0];
} else if (a[i-1][4] == a[i][4]) { // a gap
var dq = a[i][2] - a[i-1][3];
@ -2670,6 +2676,11 @@ function paf_misjoin(args)
}
} else if (i + 1 < a.length && a[i+1][4] == a[i-1][4]) { // bracketed inversion
if (ov[0] || ov[1]) ++n_inv[1];
else if (show_err) {
print("M", a[i-1].slice(0, 12).join("\t"));
print("M", a[i].slice(0, 12).join("\t"));
print("M", a[i+1].slice(0, 12).join("\t"));
}
++n_inv[0];
++i;
} else { // hanging inversion