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IndelRealigner throws a user error when it encounters reads with I operators greater than the number of read bases. 

Added test to ensure it works.
This commit is contained in:
Eric Banks 2014-04-03 18:16:24 -04:00
parent 890f4e8873
commit 7174f8cfeb
2 changed files with 13 additions and 2 deletions
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2
protected/gatk-protected/src/main/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
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@ -1462,6 +1462,8 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
case EQ: case EQ:
case X: case X:
case I: case I:
if ( fromIndex + elementLength > actualReadBases.length )
throw new UserException.MalformedBAM(read, "the CIGAR string is inconsistent with the number of bases in the read");
System.arraycopy(actualReadBases, fromIndex, readBases, toIndex, elementLength); System.arraycopy(actualReadBases, fromIndex, readBases, toIndex, elementLength);
System.arraycopy(actualBaseQuals, fromIndex, baseQuals, toIndex, elementLength); System.arraycopy(actualBaseQuals, fromIndex, baseQuals, toIndex, elementLength);
fromIndex += elementLength; fromIndex += elementLength;

13
protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java
View File

@ -47,6 +47,7 @@
package org.broadinstitute.sting.gatk.walkers.indels; package org.broadinstitute.sting.gatk.walkers.indels;
import org.broadinstitute.sting.WalkerTest; import org.broadinstitute.sting.WalkerTest;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.testng.annotations.Test; import org.testng.annotations.Test;
import java.util.Arrays; import java.util.Arrays;
@ -100,7 +101,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test @Test
public void testLods() { public void testLods() {
HashMap<String, String> e = new HashMap<String, String>(); HashMap<String, String> e = new HashMap<String, String>();
e.put( "-LOD 60", base_md5 ); e.put("-LOD 60", base_md5);
e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "4bf28d3c0337682d439257874377a681" ); e.put( "-LOD 1 --consensusDeterminationModel USE_SW", "4bf28d3c0337682d439257874377a681" );
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {
@ -148,7 +149,7 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
@Test @Test
public void testMaxReadsInMemory() { public void testMaxReadsInMemory() {
HashMap<String, String> e = new HashMap<String, String>(); HashMap<String, String> e = new HashMap<String, String>();
e.put( "--maxReadsInMemory 10000", base_md5 ); e.put("--maxReadsInMemory 10000", base_md5);
e.put( "--maxReadsInMemory 40000", base_md5 ); e.put( "--maxReadsInMemory 40000", base_md5 );
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {
@ -169,4 +170,12 @@ public class IndelRealignerIntegrationTest extends WalkerTest {
executeTest("test realigner nWayOut", spec1); executeTest("test realigner nWayOut", spec1);
} }
@Test(expectedExceptions = RuntimeException.class) // because TESTNG wraps UserExceptions in RuntimeExceptions
public void testBadCigarString() {
WalkerTestSpec spec = new WalkerTestSpec(
"-T IndelRealigner -R " + b37KGReference + " -I " + privateTestDir + "Realigner.error.bam -L 19:5787200-5787300 -targetIntervals 19:5787205-5787300 -o %s",
1,
Arrays.asList("FAILFAILFAILFAILFAILFAILFAILFAIL"));
executeTest("test bad cigar", spec);
}
} }