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Fixed issues with the integration tests: 

1) sam-jdk apparently no longer supports custom tags with type int[] values.
2) BAM output for indel cleaner integration test changed in a way that's so subtle it can't be seen after converting the output to .sam.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2439 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-12-23 23:12:22 +00:00
parent d1d6b79673
commit 98c268483e
2 changed files with 4 additions and 4 deletions
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6
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
View File

@ -274,12 +274,12 @@ public class RecalDataManager {
if( read.getReadNegativeStrandFlag() ) {
readBases = BaseUtils.simpleReverseComplement( read.getReadBases() );
}
int[] inconsistency = new int[readBases.length];
byte[] inconsistency = new byte[readBases.length];
int iii;
byte prevBase = (byte) colorSpace[0]; // The sentinel
for( iii = 0; iii < readBases.length; iii++ ) {
byte thisBase = (byte)getNextBaseFromColor( (char)prevBase, colorSpace[iii + 1] );
inconsistency[iii] = ( thisBase == readBases[iii] ? 0 : 1 );
inconsistency[iii] = (byte)( thisBase == readBases[iii] ? 0 : 1 );
prevBase = readBases[iii];
}
read.setAttribute( RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency );
@ -469,7 +469,7 @@ public class RecalDataManager {
*/
public static boolean isInconsistentColorSpace( final SAMRecord read, final int offset ) {
if( read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) != null ) {
int[] colorSpace = ((int[])read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG));
byte[] colorSpace = ((byte[])read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG));
return colorSpace[offset] != 0;
} else {
return false;

2
java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java
View File

@ -9,7 +9,7 @@ public class IntervalCleanerIntegrationTest extends WalkerTest {
@Test
public void testIntervals() {
String[] md5lod5 = {"042c1c2649a51a260bc204ec5f256c1a", "460631e8d98644dcf53b3045ca40f02a"};
String[] md5lod5 = {"4a440cbb39a8093f28f6ce66d8b9a104", "460631e8d98644dcf53b3045ca40f02a"};
WalkerTestSpec spec1 = new WalkerTestSpec(
"-T IntervalCleaner -LOD 5 -maxConsensuses 100 -greedy 100 -R /broad/1KG/reference/human_b36_both.fasta -I /humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.chrom1.SLX.SRP000032.2009_06.bam -L /humgen/gsa-scr1/GATK_Data/Validation_Data/cleaner.test.intervals --OutputCleaned %s -snps %s",
2,