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r893: added paftools.js vcfpair

This commit is contained in:
Heng Li 2018-12-01 18:53:03 -05:00
parent 2c52364527
commit eef1cee9b7
1 changed files with 101 additions and 1 deletions
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102
misc/paftools.js
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@ -1,6 +1,6 @@
#!/usr/bin/env k8
var paftools_version = '2.14-r887-dirty';
var paftools_version = '2.14-r893-dirty';
/*****************************
***** Library functions *****
@ -1197,6 +1197,105 @@ function paf_bedcov(args)
warn("# target bases overlapping regions: " + hit_len + ' (' + (100.0 * hit_len / tot_len).toFixed(2) + '%)');
}
function paf_vcfpair(args)
{
var c, is_male = false, sample = 'syndip', hgver = null;
var PAR = { '37':[[0, 2699520], [154931043, 155260560]] };
while ((c = getopt(args, "ms:g:")) != null) {
if (c == 'm') is_male = true;
else if (c == 's') sample = getopt.arg;
else if (c == 'g') hgver = getopt.arg;
}
if (is_male && (hgver == null || PAR[hgver] == null))
throw("for a male, -g must be specified to properly handle PARs on chrX");
if (getopt.ind == args.length) {
print("Usage: paftools.js vcfpair [options] <in.pair.vcf>");
print("Options:");
print(" -m the sample is male");
print(" -g STR human genome version '37' []");
print(" -s STR sample name [" + sample + "]");
exit(1);
}
var re_ctg = is_male? /^(chr)?([0-9]+|X|Y)$/ : /^(chr)?([0-9]+|X)$/;
var label = ['1', '2'];
var buf = new Bytes();
var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);
while (file.readline(buf) >= 0) {
var m, line = buf.toString();
if (line.charAt(0) == '#') {
if (/^##(source|reference)=/.test(line)) continue;
if ((m = /^##contig=.*ID=([^\s,]+)/.exec(line)) != null) {
if (!re_ctg.test(m[1])) continue;
} else if (/^#CHROM/.test(line)) {
var t = line.split("\t");
--t.length;
t[t.length-1] = sample;
line = t.join("\t");
print('##FILTER=<ID=HET1,Description="Heterozygous in the first haplotype">');
print('##FILTER=<ID=HET2,Description="Heterozygous in the second haplotype">');
print('##FILTER=<ID=GAP1,Description="Uncalled in the first haplotype">');
print('##FILTER=<ID=GAP2,Description="Uncalled in the second haplotype">');
}
print(line);
continue;
}
var t = line.split("\t");
if (!re_ctg.test(t[0])) continue;
var GT = null, AD = null, FILTER = [], HT = [null, null];
for (var i = 0; i < 2; ++i) {
if ((m = /^(\.|[0-9]+)\/(\.|[0-9]+):(\S+)/.exec(t[9+i])) == null) {
warn(line);
throw Error("malformatted VCF");
}
var s = m[3].split(",");
if (AD == null) {
AD = [];
for (var j = 0; j < s.length; ++j)
AD[j] = 0;
}
for (var j = 0; j < s.length; ++j)
AD[j] += parseInt(s[j]);
if (m[1] == '.') {
FILTER.push('GAP' + label[i]);
HT[i] = '.';
} else if (m[1] != m[2]) {
FILTER.push('HET' + label[i]);
HT[i] = '.';
} else HT[i] = m[1];
}
--t.length;
// test if this is in a haploid region
var hap = 0, st = parseInt(t[1]), en = st + t[3].length;
if (is_male) {
if (/^(chr)?X/.test(t[0])) {
if (hgver != null && PAR[hgver] != null) {
var r = PAR[hgver], in_par = false;
for (var i = 0; i < r.length; ++i)
if (r[i][0] <= st && en <= r[i][1])
in_par = true;
hap = in_par? 0 : 2;
}
} else if (/^(chr)?Y/.test(t[0])) {
hap = 1;
}
}
// special treatment for haploid regions
if (hap > 0 && FILTER.length == 1) {
if ((hap == 2 && FILTER[0] == "GAP1") || (hap == 1 && FILTER[0] == "GAP2"))
FILTER.length = 0;
}
// update VCF
t[5] = 30; // fake QUAL
t[6] = FILTER.length? FILTER.join(";") : ".";
t[9] = HT.join("|") + ":" + AD.join(",");
print(t.join("\t"));
}
file.close();
buf.destroy();
}
/**********************
* Conversion related *
**********************/
@ -2396,6 +2495,7 @@ function main(args)
else if (cmd == 'asmstat') paf_asmstat(args);
else if (cmd == 'asmgene') paf_asmgene(args);
else if (cmd == 'liftover' || cmd == 'liftOver') paf_liftover(args);
else if (cmd == 'vcfpair') paf_vcfpair(args);
else if (cmd == 'call') paf_call(args);
else if (cmd == 'mapeval') paf_mapeval(args);
else if (cmd == 'bedcov') paf_bedcov(args);