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After further review, it's unclear that my patch in RecalDataManager was the right choice. Reverting. 

Also updating other IntervalCleanerIntegrationTest failures that were masked by my first patch.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2440 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-12-24 00:32:33 +00:00
parent 98c268483e
commit 2bd0b1bbf7
2 changed files with 6 additions and 6 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() );
}
byte[] inconsistency = new byte[readBases.length];
int[] inconsistency = new int[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] = (byte)( thisBase == readBases[iii] ? 0 : 1 );
inconsistency[iii] = ( 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 ) {
byte[] colorSpace = ((byte[])read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG));
int[] colorSpace = ((int[])read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG));
return colorSpace[offset] != 0;
} else {
return false;

6
java/test/org/broadinstitute/sting/gatk/walkers/indels/IntervalCleanerIntegrationTest.java
View File

@ -16,18 +16,18 @@ public class IntervalCleanerIntegrationTest extends WalkerTest {
Arrays.asList(md5lod5));
executeTest("testLod5", spec1);
String[] md5lod200 = {"1d89ee2af03df79eb5de494c77767221", "6137bf0c25c7972b07b0d3fc6979cf5b"};
String[] md5lod200 = {"32401cef2134d973ff0037df27f1dcca", "6137bf0c25c7972b07b0d3fc6979cf5b"};
WalkerTestSpec spec2 = new WalkerTestSpec(
"-T IntervalCleaner -LOD 200 -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,
Arrays.asList(md5lod200));
executeTest("testLod200", spec2);
String[] md5cleanedOnly = {"168c8d02fceb107477381b93d189fe1f", "460631e8d98644dcf53b3045ca40f02a"};
String[] md5cleanedOnly = {"7b5a6dcc0ee770f4c8e5d0d9f36a5c34", "460631e8d98644dcf53b3045ca40f02a"};
WalkerTestSpec spec3 = new WalkerTestSpec(
"-T IntervalCleaner -LOD 5 -cleanedOnly -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,
Arrays.asList(md5cleanedOnly));
executeTest("testCleanedOnly", spec3);
}
}
}