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Merge pull request #381 from dozy/rpt_list_for_gtck
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call_gtck_composite_rpt.pl: supply rpt list to genotype check
jenniferliddle authored Nov 30, 2016

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2 parents ae94c0f + 1975777 commit 9e95d77
Showing 2 changed files with 6 additions and 3 deletions.
1 change: 1 addition & 0 deletions Changes
Original file line number Diff line number Diff line change
@@ -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
8 changes: 5 additions & 3 deletions bin/call_gtck_composite_rpt.pl
Original file line number Diff line number Diff line change
@@ -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);

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