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Merge pull request #75 from broadinstitute/eb_missing_rg_error_GSA-407 

Added better error message for BAMs with bad read groups.
This commit is contained in:
depristo 2013-02-28 05:20:39 -08:00
parent cac3f80c64 12fc198b80
commit 92d6a4f441
3 changed files with 69 additions and 5 deletions
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12
public/java/src/org/broadinstitute/sting/gatk/filters/MalformedReadFilter.java
View File

@ -28,6 +28,7 @@ package org.broadinstitute.sting.gatk.filters;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.SAMTagUtil;
import org.broadinstitute.sting.commandline.Argument;
import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
import org.broadinstitute.sting.utils.exceptions.UserException;
@ -59,9 +60,14 @@ public class MalformedReadFilter extends ReadFilter {
!checkCigarDisagreesWithAlignment(read);
}
private static boolean checkHasReadGroup(SAMRecord read) {
if ( read.getReadGroup() == null )
throw new UserException.ReadMissingReadGroup(read);
private static boolean checkHasReadGroup(final SAMRecord read) {
if ( read.getReadGroup() == null ) {
// there are 2 possibilities: either the RG tag is missing or it is not defined in the header
final String rgID = (String)read.getAttribute(SAMTagUtil.getSingleton().RG);
if ( rgID == null )
throw new UserException.ReadMissingReadGroup(read);
throw new UserException.ReadHasUndefinedReadGroup(read, rgID);
}
return true;
}

10
public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
View File

@ -276,8 +276,14 @@ public class UserException extends ReviewedStingException {
}
public static class ReadMissingReadGroup extends MalformedBAM {
public ReadMissingReadGroup(SAMRecord read) {
super(read, String.format("Read %s is either missing the read group or its read group is not defined in the BAM header, both of which are required by the GATK. Please use " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName()));
public ReadMissingReadGroup(final SAMRecord read) {
super(read, String.format("Read %s is missing the read group (RG) tag, which is required by the GATK. Please use " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName()));
}
}
public static class ReadHasUndefinedReadGroup extends MalformedBAM {
public ReadHasUndefinedReadGroup(final SAMRecord read, final String rgID) {
super(read, String.format("Read %s uses a read group (%s) that is not defined in the BAM header, which is not valid. Please use " + HelpConstants.forumPost("discussion/59/companion-utilities-replacereadgroups to fix this problem"), read.getReadName(), rgID));
}
}

52
public/java/test/org/broadinstitute/sting/gatk/filters/BadReadGroupsIntegrationTest.java 100644
View File

@ -0,0 +1,52 @@
/*
* Copyright (c) 2012 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
package org.broadinstitute.sting.gatk.filters;
import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test;
public class BadReadGroupsIntegrationTest extends WalkerTest {
@Test
public void testMissingReadGroup() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T PrintReads -R " + b36KGReference + " -I " + privateTestDir + "missingReadGroup.bam -o /dev/null",
0,
UserException.ReadMissingReadGroup.class);
executeTest("test Missing Read Group", spec);
}
@Test
public void testUndefinedReadGroup() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
"-T PrintReads -R " + b36KGReference + " -I " + privateTestDir + "undefinedReadGroup.bam -o /dev/null",
0,
UserException.ReadHasUndefinedReadGroup.class);
executeTest("test Undefined Read Group", spec);
}
}