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CycleCovariate and PrimerRoundCovariate now correctly handle negative strand 454 and SOLID reads. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2349 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2009-12-14 21:52:30 +00:00
parent c7b23d6ca5
commit 8e44bfd2ef
3 changed files with 34 additions and 18 deletions
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28
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
View File

@ -77,13 +77,22 @@ public class CycleCovariate implements StandardCovariate {
else if( read.getReadGroup().getPlatform().contains( "454" ) ) { // Some bams have "LS454" and others have just "454"
int cycle = 0;
//BUGBUG: should reverse directions on negative strand reads!
byte[] bases = read.getReadBases();
byte prevBase = bases[0];
for( int iii = 1; iii <= offset; iii++ ) {
if( bases[iii] != prevBase ) { // This base doesn't match the previous one so it is a new cycle
cycle++;
prevBase = bases[iii];
if( !read.getReadNegativeStrandFlag() ) { // forward direction
byte prevBase = bases[0];
for( int iii = 1; iii <= offset; iii++ ) {
if( bases[iii] != prevBase ) { // This base doesn't match the previous one so it is a new cycle
cycle++;
prevBase = bases[iii];
}
}
} else { // negative direction
byte prevBase = bases[bases.length-1];
for( int iii = bases.length-2; iii >= offset; iii-- ) {
if( bases[iii] != prevBase ) { // This base doesn't match the previous one so it is a new cycle
cycle++;
prevBase = bases[iii];
}
}
}
return cycle;
@ -95,8 +104,11 @@ public class CycleCovariate implements StandardCovariate {
else if( read.getReadGroup().getPlatform().equalsIgnoreCase( "SOLID" ) ) {
// The ligation cycle according to http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_057511.pdf
//BUGBUG: should reverse directions on negative strand reads!
return offset / 5; // integer division
int pos = offset;
if( read.getReadNegativeStrandFlag() ) {
pos = read.getReadLength() - (offset + 1);
}
return pos / 5; // integer division
}
//-----------------------------

6
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/PrimerRoundCovariate.java
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@ -46,7 +46,11 @@ public class PrimerRoundCovariate implements ExperimentalCovariate {
// Used to pick out the covariate's value from attributes of the read
public final Comparable getValue( final SAMRecord read, final int offset ) {
if( read.getReadGroup().getPlatform().equalsIgnoreCase( "SOLID" ) ) {
return offset % 5; // the primer round according to http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_057511.pdf
int pos = offset;
if( read.getReadNegativeStrandFlag() ) {
pos = read.getReadLength() - (offset + 1);
}
return pos % 5; // the primer round according to http://www3.appliedbiosystems.com/cms/groups/mcb_marketing/documents/generaldocuments/cms_057511.pdf
} else {
return 1; // nothing to do here because it is always the same
}

18
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -17,9 +17,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
public void testCountCovariates1() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12892.SLX.SRP000031.2009_06.selected.bam", "16f87c9644b27c3c3fe7a963eed45d2d" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "602bc582a0e5507fee806db19f07b180");
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "92b7ec1f3b5d33eb86be8298827d55f5" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "3caf6ec9c38ce78284159b279b0de0c0" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "add8196af03d5a674aa3de702995cbbf");
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "b039f405580ad844cd1dfd4d8ba25913" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "c730bff43ffb89dcb0774926286cac6f" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -50,9 +50,9 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
public void testTableRecalibrator1() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12892.SLX.SRP000031.2009_06.selected.bam", "d7f3e0db5ed9fefc917144a0f937d50d" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "94f2c602fef9800e270326be9faab3ad");
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "320ff4cbf8f1e73ba2d6e93567382684" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "e9a7ac8bc7c6b3daaf7f80730046318d" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "fb82046d5acfb07625d5459526d5f6c8");
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "3fe6ee95cfa6155f8cc8e3e0a6330ad2" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "e4eae955f7d408b2af34c9224616f564" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -80,7 +80,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesVCF() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "1a2762916473bd037c72125c35d274d6");
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "d0bdd1934f003406e93f935b63ab6edd");
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -108,7 +108,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testCountCovariatesNoReadGroups() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "437a6dd63c61d2814f42129ce393d7ce" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "fadfa35415a694781ed2b4d1b1d9535b" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();
@ -138,7 +138,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test
public void testTableRecalibratorNoReadGroups() {
HashMap<String, String> e = new HashMap<String, String>();
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "9bbb281c4f55b0c094457e9f69e61962" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "4879036295b567514f637d21030bf9c8" );
for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey();