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evaluate large-scale misjoins

This commit is contained in:
Heng Li 2021-02-07 12:34:13 -05:00
parent 1025993469
commit 75c8933511
1 changed files with 110 additions and 1 deletions
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111
misc/paftools.js
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@ -2591,6 +2591,113 @@ function paf_vcfstat(args)
print("# >=7000 deletions: " + x.delinf);
}
function paf_parseNum(s) {
var m, x = null;
if ((m = /^(\d*\.?\d*)([mMgGkK]?)/.exec(s)) != null) {
x = parseFloat(m[1]);
if (m[2] == 'k' || m[2] == 'K') x *= 1000;
else if (m[2] == 'm' || m[2] == 'M') x *= 1000000;
else if (m[2] == 'g' || m[2] == 'G') x *= 1000000000;
}
return Math.floor(x + .499);
}
function paf_misjoin(args)
{
var c, min_seg_len = 1000000, max_gap = 1000000, fn_cen = null, show_long = 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) {
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;
}
if (args.length == getopt.ind) {
print("Usage: paftools.js misjoin [options] <in.paf>");
print("Options:");
print(" -c FILE BED for centromeres []");
print(" -l NUM min alignment block length [1m]");
print(" -g NUM max gap size [1m]");
print(" -p output long alignment blocks for debugging");
return;
}
var cen = {};
var file, buf = new Bytes();
if (fn_cen != null) {
file = new File(fn_cen);
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
if (cen[t[0]] == null) cen[t[0]] = [];
cen[t[0]].push([parseInt(t[1]), parseInt(t[2])]);
}
file.close();
}
function test_cen(cen, chr, st, en) {
var b = cen[chr];
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;
}
function process(a) {
var k = 0;
for (var i = 0; i < a.length; ++i) {
for (var j = 1; j <= 3; ++j) a[i][j] = parseInt(a[i][j]);
for (var j = 6; j <= 11; ++j) a[i][j] = parseInt(a[i][j]);
if (a[i][10] >= min_seg_len) a[k++] = a[i];
}
a.length = k;
if (a.length == 1) return;
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];
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]);
if (a[i-1][5] != a[i][5]) { // different chr
if (ov[0] || ov[1]) ++n_diff[1];
++n_diff[0];
} else if (a[i-1][4] == a[i][4]) { // a gap
var dq = a[i][2] - a[i-1][3];
var dr = a[i][4] == '+'? a[i][7] - a[i-1][8] : a[i-1][7] - a[i][8];
var gap = dr > dq? dr - dq : dq - dr;
if (gap > max_gap) {
if (ov[0] || ov[1]) ++n_gap[1];
++n_gap[0];
}
} else if (i + 1 < a.length && a[i+1][4] == a[i-1][4]) { // bracketed inversion
if (ov[0] || ov[1]) ++n_inv[1];
++n_inv[0];
++i;
} else { // hanging inversion
if (ov[0] || ov[1]) ++n_inv_end[1];
++n_inv_end[0];
}
}
}
file = args[getopt.ind] == "-"? new File() : new File(args[getopt.ind]);
var a = [];
while (file.readline(buf) >= 0) {
var t = buf.toString().split("\t");
if (a.length > 0 && a[0][0] != t[0]) {
process(a);
a.length = 0;
}
a.push(t);
}
if (a.length > 0) process(a);
file.close();
buf.destroy();
print("# inter-chromosomal misjoins: " + n_diff.join(","));
print("# intra-chromosomal gaps: " + n_gap.join(","));
print("# candidate inversions in the middle: " + n_inv.join(","));
print("# candidate inversions at contig ends: " + n_inv_end.join(","));
}
/*************************
***** main function *****
*************************/
@ -2608,7 +2715,8 @@ function main(args)
print("");
print(" stat collect basic mapping information in PAF/SAM");
print(" asmstat collect basic assembly information");
print(" asmgene evaluate gene completeness (EXPERIMENTAL)");
print(" asmgene evaluate gene completeness");
print(" misjoin evaluate large-scale misjoins");
print(" liftover simplistic liftOver");
print(" call call variants from asm-to-ref alignment with the cs tag");
print(" bedcov compute the number of bases covered");
@ -2632,6 +2740,7 @@ function main(args)
else if (cmd == 'stat') paf_stat(args);
else if (cmd == 'asmstat') paf_asmstat(args);
else if (cmd == 'asmgene') paf_asmgene(args);
else if (cmd == 'misjoin') paf_misjoin(args);
else if (cmd == 'liftover' || cmd == 'liftOver') paf_liftover(args);
else if (cmd == 'vcfpair') paf_vcfpair(args);
else if (cmd == 'call') paf_call(args);