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Add -s sample option for VCF output

This commit is contained in:
Torsten Seemann 2018-09-19 14:54:37 -04:00 committed by Heng Li
parent 8b12da8b0f
commit 34be359e25
1 changed files with 5 additions and 3 deletions
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8
misc/paftools.js
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@ -341,14 +341,15 @@ function paf_call(args)
{
var re_cs = /([:=*+-])(\d+|[A-Za-z]+)/g, re_tag = /\t(\S\S:[AZif]):(\S+)/g;
var c, min_cov_len = 10000, min_var_len = 50000, gap_thres = 50, gap_thres_long = 1000, min_mapq = 5;
var fa_tmp = null, fa, fa_lens, is_vcf = false;
while ((c = getopt(args, "l:L:g:q:B:f:")) != null) {
var fa_tmp = null, fa, fa_lens, is_vcf = false, sample_name = "sample";
while ((c = getopt(args, "l:L:g:q:B:f:s:")) != null) {
if (c == 'l') min_cov_len = parseInt(getopt.arg);
else if (c == 'L') min_var_len = parseInt(getopt.arg);
else if (c == 'g') gap_thres = parseInt(getopt.arg);
else if (c == 'G') gap_thres_long = parseInt(getopt.arg);
else if (c == 'q') min_mapq = parseInt(getopt.arg);
else if (c == 'f') fa_tmp = fasta_read(getopt.arg, fa_lens);
else if (c == 's') sample_name = getopt.arg;
}
if (fa_tmp != null) fa = fa_tmp[0], fa_lens = fa_tmp[1], is_vcf = true;
@ -360,6 +361,7 @@ function paf_call(args)
print(" -q INT min mapping quality ["+min_mapq+"]");
print(" -g INT short/long gap threshold (for statistics only) ["+gap_thres+"]");
print(" -f FILE reference sequences (enabling VCF output) [null]");
print(" -s NAME sample name in VCF header ["+sample_name+"]");
exit(1);
}
@ -423,7 +425,7 @@ function paf_call(args)
print('##INFO=<ID=QSTART,Number=1,Type=Integer,Description="Query start">');
print('##INFO=<ID=QSTRAND,Number=1,Type=String,Description="Query strand">');
print('##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">');
print('#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sample');
print('#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT '+sample_name);
}
var a = [], out = [];