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Un-reverted Matt's previous changes and fixed integration tests. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2441 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-24 02:47:00 +00:00
parent 2bd0b1bbf7
commit 6df40876a3
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() ) { if( read.getReadNegativeStrandFlag() ) {
readBases = BaseUtils.simpleReverseComplement( read.getReadBases() ); readBases = BaseUtils.simpleReverseComplement( read.getReadBases() );
} }
int[] inconsistency = new int[readBases.length]; byte[] inconsistency = new byte[readBases.length];
int iii; int iii;
byte prevBase = (byte) colorSpace[0]; // The sentinel byte prevBase = (byte) colorSpace[0]; // The sentinel
for( iii = 0; iii < readBases.length; iii++ ) { for( iii = 0; iii < readBases.length; iii++ ) {
byte thisBase = (byte)getNextBaseFromColor( (char)prevBase, colorSpace[iii + 1] ); 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]; prevBase = readBases[iii];
} }
read.setAttribute( RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG, inconsistency ); 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 ) { public static boolean isInconsistentColorSpace( final SAMRecord read, final int offset ) {
if( read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) != null ) { 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; return colorSpace[offset] != 0;
} else { } else {
return false; return false;

6
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -49,10 +49,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test @Test
public void testTableRecalibrator1() { public void testTableRecalibrator1() {
HashMap<String, String> e = new HashMap<String, String>(); HashMap<String, String> e = new HashMap<String, String>();
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12892.SLX.SRP000031.2009_06.selected.bam", "8d68e99f5ef1138f25893a6b2725d2e9" ); e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12892.SLX.SRP000031.2009_06.selected.bam", "a3d4153765625a451bee768ad46775b3" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "5954b7246d2e0c5c65267026819d5933"); e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "5954b7246d2e0c5c65267026819d5933");
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "91fd3c557db56fd969523d8c06d71a0b" ); e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "91fd3c557db56fd969523d8c06d71a0b" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "7dd4c6a3f318a1dccb3f33d08bff953b" ); e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "9655f57949b01d6ee8a7c9b92e61a47f" );
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey(); String bam = entry.getKey();
@ -193,7 +193,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test @Test
public void testTableRecalibratorNoIndex() { public void testTableRecalibratorNoIndex() {
HashMap<String, String> e = new HashMap<String, String>(); HashMap<String, String> e = new HashMap<String, String>();
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "dd8705b54f0ffbedb689608221ade13a" ); e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.noindex.bam", "33cb41fa3e959ac15ac9af329167a736" );
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey(); String bam = entry.getKey();