From 831ad0cd1af490b93a0e36fd42c3e5d20dac960c Mon Sep 17 00:00:00 2001
From: ebanks <ebanks@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Fri, 22 Apr 2011 13:23:33 +0000
Subject: [PATCH] Quit immediately with an error message if any of the
 individual steps fails.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5677 348d0f76-0448-11de-a6fe-93d51630548a
---
 perl/liftOverVCF.pl | 11 ++++++++---
 1 file changed, 8 insertions(+), 3 deletions(-)

diff --git a/perl/liftOverVCF.pl b/perl/liftOverVCF.pl
index a03a4fe16..7039e111f 100755
--- a/perl/liftOverVCF.pl
+++ b/perl/liftOverVCF.pl
@@ -40,7 +40,7 @@ my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $old
 if ($recordOriginalLocation) {
   $cmd .= " -recordOriginalLocation";
 }
-system($cmd);
+system($cmd) == 0 or quit("The liftover step failed.  Please correct the necessary errors before retrying.");
 
 # we need to sort the lifted over file now
 print "\nRe-sorting the vcf...\n";
@@ -62,12 +62,12 @@ close(UNSORTED);
 close(SORTED);
 
 $cmd = "grep \"^#\" -v $unsorted_vcf | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai >> $sorted_vcf";
-system($cmd);
+system($cmd) == 0 or quit("The sorting step failed.  Please correct the necessary errors before retrying.");
 
 # Filter the VCF for bad records
 print "\nFixing/removing bad records...\n";
 $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T FilterLiftedVariants -R $newRef.fasta -B:variant,vcf $sorted_vcf -o $out";
-system($cmd);
+system($cmd) == 0 or quit("The filtering step failed.  Please correct the necessary errors before retrying.");
 
 # clean up
 unlink $unsorted_vcf;
@@ -76,3 +76,8 @@ my $sorted_index = "$sorted_vcf.idx";
 unlink $sorted_index;
 
 print "\nDone!\n";
+
+sub quit {
+    print "\n$_[0]\n";
+    exit(1);
+}