added option to call all contigs

lh3 · Jun 6, 2021 · 68ddbc4 · 68ddbc4
1 parent c735fdb
commit 68ddbc4
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Showing 2 changed files with 12 additions and 7 deletions.
diff --git a/dipcall-aux.js b/dipcall-aux.js
@@ -1,6 +1,6 @@
 #!/usr/bin/env k8
 
-var version = "0.1";
+var version = "0.3";
 
 var getopt = function(args, ostr) {
 	var oli; // option letter list index
@@ -42,16 +42,18 @@ var getopt = function(args, ostr) {
 
 function vcfpair(args)
 {
-	var c, is_male = false, sample = 'syndip', fn_par = null, par = null;
-	while ((c = getopt(args, "ms:p:")) != null) {
+	var c, is_male = false, sample = 'syndip', fn_par = null, par = null, all_ctg = false;
+	while ((c = getopt(args, "ams:p:")) != null) {
 		if (c == 's') sample = getopt.arg;
 		else if (c == 'p') fn_par = getopt.arg, is_male = true;
+		else if (c == 'a') all_ctg = true;
 	}
 	if (getopt.ind == args.length) {
 		print("Usage: dipcall-aux.js vcfpair [options] <in.pair.vcf>");
 		print("Options:");
 		print("  -p FILE  chrX PAR; assuming male sample []");
 		print("  -s STR   sample name [" + sample + "]");
+		print("  -a       call on all contigs regardless of naming");
 		exit(1);
 	}
 
@@ -68,7 +70,7 @@ function vcfpair(args)
 		file.close();
 	}
 
-	var re_ctg = is_male? /^(chr)?([0-9]+|X|Y)$/ : /^(chr)?([0-9]+|X)$/;
+	var re_ctg = all_ctg? /^\S+$/ : is_male? /^(chr)?([0-9]+|X|Y)$/ : /^(chr)?([0-9]+|X)$/;
 	var label = ['1', '2'];
 	var buf = new Bytes();
 	var file = args[getopt.ind] == '-'? new File() : new File(args[getopt.ind]);

diff --git a/run-dipcall b/run-dipcall
@@ -7,12 +7,13 @@ use Getopt::Std;
 my $version = "0.3";
 
 my %opts = (t=>8);
-getopts("t:d:x:muz:W:", \%opts);
+getopts("t:d:x:muz:W:a", \%opts);
 
 die("Usage: run-dipcall [options] <prefix> <ref.fa> <pat.fa> <mat.fa>
 Options:
   -t INT     number of threads [$opts{t}]
   -d FILE    unimap/minimap2 index for ref.fa []
+  -a         call on all contigs regardless of naming
   -x FILE    PAR on chrX; assuming male
   -z INT     Z-drop [mapper default]
   -m         use minimap2 for mapping (default)
@@ -87,10 +88,12 @@ push(@mak, "");
 push(@mak, "$pre.pair.vcf.gz:$pre.hap1.bam $pre.hap2.bam");
 push(@mak, q{	$(ROOT)/htsbox pileup -q5 -evcf $(REF_FA) $^ | $(ROOT)/htsbox bgzip > $@});
 push(@mak, "$pre.dip.vcf.gz:$pre.pair.vcf.gz");
+
+my $pair_opt = defined($opts{a})? "-a" : "";
 if ($is_male) {
-	push(@mak, q{	$(ROOT)/k8 $(ROOT)/dipcall-aux.js vcfpair } . qq{-p $opts{x}} . q{ $< | $(ROOT)/htsbox bgzip > $@});
+	push(@mak, q{	$(ROOT)/k8 $(ROOT)/dipcall-aux.js vcfpair} . qq{ $pair_opt -p $opts{x} } . q{$< | $(ROOT)/htsbox bgzip > $@});
 } else {
-	push(@mak, q{	$(ROOT)/k8 $(ROOT)/dipcall-aux.js vcfpair $< | $(ROOT)/htsbox bgzip > $@});
+	push(@mak, q{	$(ROOT)/k8 $(ROOT)/dipcall-aux.js vcfpair} . qq{ $pair_opt } . q{$< | $(ROOT)/htsbox bgzip > $@});
 }
 push(@mak, "");