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Removing the obsolete --hapmap and --hapmap_chip options 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4172 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-08-31 16:57:05 +00:00
parent b33873206a
commit 3d6c4fc55f
4 changed files with 5 additions and 30 deletions
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7
java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
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@ -371,14 +371,7 @@ public class GenomeAnalysisEngine {
validateSuppliedReferenceAgainstWalker(my_walker, argCollection);
referenceDataSource = openReferenceSequenceFile(argCollection.referenceFile);
//
// please don't use these in the future, use the new syntax <- if we're not using these please remove them
//
if (argCollection.DBSNPFile != null) bindConvenienceRods(DbSNPHelper.STANDARD_DBSNP_TRACK_NAME, "dbsnp", argCollection.DBSNPFile);
if (argCollection.HAPMAPFile != null)
bindConvenienceRods("hapmap", "HapMapAlleleFrequencies", argCollection.HAPMAPFile);
if (argCollection.HAPMAPChipFile != null)
bindConvenienceRods("hapmap-chip", "GFF", argCollection.HAPMAPChipFile);
// TODO: The ROD iterator currently does not understand multiple intervals file. Fix this by cleaning the ROD system.
if (argCollection.intervals != null && argCollection.intervals.size() == 1) {
bindConvenienceRods("interval", "Intervals", argCollection.intervals.get(0).replaceAll(",", ""));

15
java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
View File

@ -33,7 +33,6 @@ import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.commandline.Input;
import org.broadinstitute.sting.gatk.DownsampleType;
import org.broadinstitute.sting.gatk.DownsamplingMethod;
import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMReaderID;
import org.broadinstitute.sting.utils.interval.IntervalSetRule;
import org.simpleframework.xml.*;
import org.simpleframework.xml.core.Persister;
@ -111,14 +110,6 @@ public class GATKArgumentCollection {
@Input(fullName = "DBSNP", shortName = "D", doc = "DBSNP file", required = false)
public String DBSNPFile = null;
@Element(required = false)
@Input(fullName = "hapmap", shortName = "H", doc = "Hapmap file", required = false)
public String HAPMAPFile = null;
@Element(required = false)
@Input(fullName = "hapmap_chip", shortName = "hc", doc = "Hapmap chip file", required = false)
public String HAPMAPChipFile = null;
/**
* The override mechanism in the GATK, by default, populates the command-line arguments, then
* the defaults from the walker annotations. Unfortunately, walker annotations should be trumped
@ -315,12 +306,6 @@ public class GATKArgumentCollection {
if (!other.DBSNPFile.equals(this.DBSNPFile)) {
return false;
}
if (!other.HAPMAPFile.equals(this.HAPMAPFile)) {
return false;
}
if (!other.HAPMAPChipFile.equals(this.HAPMAPChipFile)) {
return false;
}
if (!other.unsafe.equals(this.unsafe)) {
return false;
}

3
java/test/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollectionUnitTest.java
View File

@ -1,7 +1,6 @@
package org.broadinstitute.sting.gatk.arguments;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
import org.junit.After;
import static org.junit.Assert.fail;
import org.junit.Before;
@ -83,8 +82,6 @@ public class GATKArgumentCollectionUnitTest extends BaseTest {
collect.strictnessLevel = SAMFileReader.ValidationStringency.STRICT;
collect.referenceFile = new File("referenceFile".toLowerCase());
collect.DBSNPFile = "DBSNPFile".toLowerCase();
collect.HAPMAPFile = "HAPMAPFile".toLowerCase();
collect.HAPMAPChipFile = "HAPMAPChipFile".toLowerCase();
collect.unsafe = ValidationExclusion.TYPE.ALL;
collect.downsampleFraction = null;
collect.downsampleCoverage = null;

10
perl/runReleaseSanityCheck.pl
View File

@ -31,23 +31,23 @@ $command = "$command_prefix -T TableRecalibration -I /humgen/gsa-hpprojects/GATK
run($command, $dry);
print "Executing IndelRealignerWholeExome...";
$command = "$command_prefix -T IndelRealigner -LOD 5 -maxConsensuses 100 -greedy 100 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L chr1:900,000-1,000,000 -compress 1 -targetIntervals /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.realigner.intervals -O $tmp_bam";
$command = "$command_prefix -T IndelRealigner -LOD 5 -maxConsensuses 100 -greedy 100 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.bam -L chr1:900,000-1,000,000 -compress 1 -targetIntervals /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.ESP.WEx.chr1.realigner.intervals -o $tmp_bam";
run($command, $dry);
print "Executing IndelRealignerWholeGenome...";
$command = "$command_prefix -T IndelRealigner -LOD 5 -maxConsensuses 100 -greedy 100 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:975,000-1,000,000 -compress 1 -targetIntervals /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.realigner.intervals -O $tmp_bam";
$command = "$command_prefix -T IndelRealigner -LOD 5 -maxConsensuses 100 -greedy 100 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:975,000-1,000,000 -compress 1 -targetIntervals /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.realigner.intervals -o $tmp_bam";
run($command, $dry);
print "Executing UnifiedGenotyperWholeExome...";
$command = "$command_prefix -T UnifiedGenotyper -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 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -varout /dev/null -XL chr1:1,500,000-247179187";
$command = "$command_prefix -T UnifiedGenotyper -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 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -o /dev/null -XL chr1:1,500,000-247179187";
run($command, $dry);
print "Executing UnifiedGenotyperWholeGenome...";
$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:750,000-1,000,000 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -varout /dev/null";
$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:750,000-1,000,000 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -o /dev/null";
run($command, $dry);
print "Executing UnifiedGenotyperWholeGenomeMultithreaded...";
$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:500,000-1,000,000 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -varout /dev/null -nt 4";
$command = "$command_prefix -T UnifiedGenotyper -I /humgen/gsa-hpprojects/GATK/data/Evaluation_Data/NA12878.GAII.chr1.50MB.bam -L chr1:500,000-1,000,000 -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod -o /dev/null -nt 4";
run($command, $dry);
unlink $tmp_bam;