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improved sveval

This commit is contained in:
Heng Li 2021-03-06 19:44:13 -05:00
parent 4dfd495cc2
commit ecbc399fa2
1 changed files with 12 additions and 9 deletions
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21
misc/paftools.js
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@ -2711,17 +2711,19 @@ function paf_misjoin(args)
function paf_sveval(args)
{
var c, min_flt = 30, min_size = 50, max_size = 10000, win_size = 500, print_err = false;
while ((c = getopt(args, "f:i:x:w:e")) != null) {
var c, min_flt = 30, min_size = 50, max_size = 10000, win_size = 500, print_err = false, bed_fn = null;
while ((c = getopt(args, "f:i:x:w:er:")) != null) {
if (c == 'f') min_flt = paf_parseNum(getopt.arg);
else if (c == 'i') min_size = paf_parseNum(getopt.arg);
else if (c == 'x') max_size = paf_parseNum(getopt.arg);
else if (c == 'w') win_size = paf_parseNum(getopt.arg);
else if (c == 'r') bed_fn = getopt.arg;
else if (c == 'e') print_err = true;
}
if (args.length - getopt.ind < 3) {
print("Usage: paftools.js sveval [options] <conf.bed> <base.vcf> <call.vcf>");
if (args.length - getopt.ind < 2) {
print("Usage: paftools.js sveval [options] <base.vcf> <call.vcf>");
print("Options:");
print(" -r FILE confident region in BED []");
print(" -f INT min length to discard [" + min_flt + "]");
print(" -i INT min SV length [" + min_size + "]");
print(" -x INT max SV length [" + max_size + "]");
@ -2749,7 +2751,7 @@ function paf_sveval(args)
return bed;
}
var bed = read_bed(args[getopt.ind]);
var bed = bed_fn != null? read_bed(bed_fn) : null;
function read_vcf(fn, bed) {
var buf = new Bytes();
@ -2758,12 +2760,13 @@ function paf_sveval(args)
while (file.readline(buf) >= 0) {
var m, t = buf.toString().split("\t");
if (t[0][0] == '#') continue;
if (bed[t[0]] == null) continue;
if (bed != null && bed[t[0]] == null) continue;
if (t[4] == '<INV>' || t[4] == '<INVDUP>') continue; // no inversion
if (/[\[\]]/.test(t[4])) continue; // no break points
var st = parseInt(t[1]) - 1, en = st + t[3].length;
if ((m = /((;END)|(^END))=(\d+)/.exec(t[7])) != null)
en = parseInt(m[4]);
if (Interval.find_ovlp(bed[t[0]], st, en).length == 0) continue;
if (bed != null && Interval.find_ovlp(bed[t[0]], st, en).length == 0) continue;
// determine svlen
var s = t[4].split(","), max_del = 0, max_ins = 0;
for (var i = 0; i < s.length; ++i) {
@ -2809,8 +2812,8 @@ function paf_sveval(args)
return [n, m];
}
var v_base = read_vcf(args[getopt.ind+1], bed);
var v_call = read_vcf(args[getopt.ind+2], bed);
var v_base = read_vcf(args[getopt.ind+0], bed);
var v_call = read_vcf(args[getopt.ind+1], bed);
var fn = compare_vcf(v_call, v_base, 'FN');
var fp = compare_vcf(v_base, v_call, 'FP');
print('SN', fn[0], fn[1], (fn[1] / fn[0]).toFixed(6));