diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java index ce7d7c911..652f0d322 100644 --- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java @@ -52,6 +52,9 @@ public class DoCOutputType { if(partition == null) return baseName; + if(baseName.trim().equals("/dev/null")) + return "/dev/null"; + // mhanna 22 Aug 2010 - Deliberately force this header replacement to make sure integration tests pass. // TODO: Update integration tests and get rid of this. String partitionType = (partition == DoCOutputType.Partition.readgroup ? "read_group" : partition.toString()); diff --git a/perl/runReleaseSanityCheck.pl b/perl/runReleaseSanityCheck.pl index bc9edd194..c237cbf4f 100755 --- a/perl/runReleaseSanityCheck.pl +++ b/perl/runReleaseSanityCheck.pl @@ -14,6 +14,10 @@ $command_prefix = "java -Xmx4096m -jar $sting -R /seq/references/Homo_sapiens_as $random_number = rand(); $tmp_bam = "/tmp/$random_number.bam"; +print "Executing DepthOfCoverage..."; +$command = "$command_prefix -T DepthOfCoverage -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L chr1:10000000-10100000 -o /dev/null"; +run($command, $dry); + print "Executing CountCovariatesWholeExome..."; $command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -standard -OQ -recalFile /dev/null -XL chr1:1,000,000-247179187"; run($command, $dry); @@ -23,11 +27,11 @@ $command = "$command_prefix -T CountCovariates -I /humgen/gsa-hpprojects/GATK/da run($command, $dry); print "Executing TableRecalibratorWholeExome..."; -$command = "$command_prefix -T TableRecalibration -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -OQ -recalFile /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.recal.csv -outputBam $tmp_bam -XL chr1:1,000,000-247179187"; +$command = "$command_prefix -T TableRecalibration -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/whole_exome_agilent_designed_120.targets.chr1.interval_list -OQ -recalFile /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.recal.csv --out $tmp_bam -XL chr1:1,000,000-247179187"; run($command, $dry); print "Executing TableRecalibratorWholeGenome..."; -$command = "$command_prefix -T TableRecalibration -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:1,950,000-2,000,000 -OQ -recalFile /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.recal.csv -outputBam $tmp_bam"; +$command = "$command_prefix -T TableRecalibration -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:1,950,000-2,000,000 -OQ -recalFile /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.recal.csv --out $tmp_bam"; run($command, $dry); print "Executing IndelRealignerWholeExome...";