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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
This commit is contained in:
ebanks 2011-04-22 13:23:33 +00:00
parent 88735a8c9b
commit 831ad0cd1a
1 changed files with 8 additions and 3 deletions
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11
perl/liftOverVCF.pl
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@ -40,7 +40,7 @@ my $cmd = "java -jar $gatk/dist/GenomeAnalysisTK.jar -T LiftoverVariants -R $old
if ($recordOriginalLocation) { if ($recordOriginalLocation) {
$cmd .= " -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 # we need to sort the lifted over file now
print "\nRe-sorting the vcf...\n"; print "\nRe-sorting the vcf...\n";
@ -62,12 +62,12 @@ close(UNSORTED);
close(SORTED); close(SORTED);
$cmd = "grep \"^#\" -v $unsorted_vcf | sort -n -k2 -T $tmp | $gatk/perl/sortByRef.pl --tmp $tmp - $newRef.fasta.fai >> $sorted_vcf"; $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 # Filter the VCF for bad records
print "\nFixing/removing bad records...\n"; 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"; $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 # clean up
unlink $unsorted_vcf; unlink $unsorted_vcf;
@ -76,3 +76,8 @@ my $sorted_index = "$sorted_vcf.idx";
unlink $sorted_index; unlink $sorted_index;
print "\nDone!\n"; print "\nDone!\n";
sub quit {
print "\n$_[0]\n";
exit(1);
}