call_gtck_composite_rpt.pl: supply rpt list to genotype check

Changes

@@ -7,6 +7,7 @@ LIST OF CHANGES FOR NPG-QC PACKAGE
  - add perl 5.22-shrplib to travis matrix
  - to reduce uncertainty in ranking close results, increase precision
    used for ranking contamination results
+ - call_gtck_composite_rpt.pl - supply rpt list to genotype check
 
 release 62.5
  - a very concise replacement for NPG_QC pages

bin/call_gtck_composite_rpt.pl

@@ -49,8 +49,9 @@
 ##########
 my @bam_file_list;
 my $ext = $opts{c}? q[cram]: q[bam];
-if($opts{r}) {
-	@bam_file_list = map { my ($r, $p, $t) = (split ":", $_); find_runlanefolder($r, $p, $t, $ext) or sprintf "irods:/seq/%d/%d_%d%s.%s", $r, $r, $p, $t? "#$t": "", $ext; } (split ";", $opts{r});
+my $rpt_list = $opts{r};
+if($rpt_list) {
+	@bam_file_list = map { my ($r, $p, $t) = (split ":", $_); find_runlanefolder($r, $p, $t, $ext) or sprintf "irods:/seq/%d/%d_%d%s.%s", $r, $r, $p, $t? "#$t": "", $ext; } (split ";", $rpt_list);
 
 	carp qq[bam_file_list:\n\t], join("\n\t", @bam_file_list), "\n";
 }
@@ -92,7 +93,6 @@
 	alignments_in_bam => 1,
 	reference_fasta => $reference_genome,
 	input_files => [ (@bam_file_list) ],
-	path => q[.],
 );
 if(defined $plex_name) {
 	$attribs{sequenom_plex} = $plex_name;
@@ -109,6 +109,8 @@
 	$attribs{genotype_executables_path} = $gt_exec_path;
 }
 
+$attribs{rpt_list} = $rpt_list;
+
 my $gtck= npg_qc::autoqc::checks::genotype->new(%attribs);
 
 exit 0 unless($gtck->can_run);