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r1132: document misjoin output 

Also additional check of centromeric breakpoints
This commit is contained in:
Heng Li 2022-05-11 21:39:29 -04:00
parent e018caea32
commit 31de4fd1bc
1 changed files with 28 additions and 6 deletions
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34
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8
var paftools_version = '2.24-r1122';
var paftools_version = '2.24-r1132-dirty';
/*****************************
***** Library functions *****
@ -2704,6 +2704,24 @@ function paf_misjoin(args)
return len < (en - st) * cen_ratio? false : true;
}
function test_cen_point(cen, chr, x) {
var b = cen[chr];
if (b == null) return false;
print(x, b[0][0], b[0][1]);
for (var j = 0; j < b.length; ++j)
if (x >= b[j][0] && x < b[j][1])
return true;
return false;
}
if (show_err || show_long) {
print("C\tJ inter-chromosomal misjoin");
print("C\tj inter-chromosomal misjoin with both breakpoints ending in centromeres");
print("C\tG long gap on the reference genome");
print("C\tg long gap on the reference genome with both breakpoints ending in centromeres");
print("C\tM closed inversion");
print("C");
}
function process(a) {
var k = 0;
for (var i = 0; i < a.length; ++i) {
@ -2716,14 +2734,17 @@ function paf_misjoin(args)
a = a.sort(function(x,y){return x[2]-y[2]});
if (show_long) for (var i = 0; i < a.length; ++i) print(a[i].join("\t"));
for (var i = 1; i < a.length; ++i) {
var ov = [false, false];
var ov = [false, false], end_cen = [false, false];
ov[0] = test_cen(cen, a[i-1][5], a[i-1][7], a[i-1][8]);
ov[1] = test_cen(cen, a[i][5], a[i][7], a[i][8]);
end_cen[0] = test_cen_point(cen, a[i-1][5], a[i-1][4] == '+'? a[i-1][8] : a[i-1][7]);
end_cen[1] = test_cen_point(cen, a[i][5], a[i][4] == '+'? 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"));
var label = end_cen[0] && end_cen[1]? 'j' : 'J';
print(label, a[i-1].slice(0, 12).join("\t"));
print(label, a[i].slice(0, 12).join("\t"));
}
++n_diff[0];
} else if (a[i-1][4] == a[i][4]) { // a gap
@ -2733,8 +2754,9 @@ function paf_misjoin(args)
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"));
var label = end_cen[0] && end_cen[1]? 'g' : 'G';
print(label, a[i-1].slice(0, 12).join("\t"));
print(label, a[i].slice(0, 12).join("\t"));
}
++n_gap[0];
}