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- Update DoC to support output to /dev/null. 

- Add a release sanity check for DoC.
- Update release sanity checks with new command-line argument system.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4236 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2010-09-08 23:43:18 +00:00
parent 1b1ec7e52d
commit 5119bdb55e
2 changed files with 9 additions and 2 deletions
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3
java/src/org/broadinstitute/sting/gatk/walkers/coverage/DoCOutputType.java
View File

@ -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());

8
perl/runReleaseSanityCheck.pl
View File

@ -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...";