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I'm making this change now (as opposed to waiting until Monday) to honor Tim's request. 

The cycle covariate is now first/second of pair aware.  I'm taking it on faith from both Chris Hartl (waiting on slides from him) and Tim that this is the right thing to do.  We'll have Ryan confirm it all next week.
The only change is that if a read is the second of a pair, we multiple the cycle by -1 (a simple way of separating its index from that of its mate).
Of course, this broke all integration tests.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2431 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-23 16:26:43 +00:00
parent e29e8e52b9
commit 872a9d1c7b
2 changed files with 22 additions and 17 deletions
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17
java/src/org/broadinstitute/sting/gatk/walkers/recalibration/CycleCovariate.java
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@ -60,16 +60,17 @@ public class CycleCovariate implements StandardCovariate {
// Used to pick out the covariate's value from attributes of the read // Used to pick out the covariate's value from attributes of the read
public final Comparable getValue( final SAMRecord read, final int offset ) { public final Comparable getValue( final SAMRecord read, final int offset ) {
int cycle = 0;
//----------------------------- //-----------------------------
// ILLUMINA // ILLUMINA
//----------------------------- //-----------------------------
if( read.getReadGroup().getPlatform().equalsIgnoreCase( "ILLUMINA" ) ) { if( read.getReadGroup().getPlatform().equalsIgnoreCase( "ILLUMINA" ) ) {
int cycle = offset; cycle = offset;
if( read.getReadNegativeStrandFlag() ) { if( read.getReadNegativeStrandFlag() ) {
cycle = read.getReadLength() - (offset + 1); cycle = read.getReadLength() - (offset + 1);
} }
return cycle;
} }
//----------------------------- //-----------------------------
@ -77,7 +78,6 @@ public class CycleCovariate implements StandardCovariate {
//----------------------------- //-----------------------------
else if( read.getReadGroup().getPlatform().contains( "454" ) ) { // Some bams have "LS454" and others have just "454" else if( read.getReadGroup().getPlatform().contains( "454" ) ) { // Some bams have "LS454" and others have just "454"
int cycle = 0;
byte[] bases = read.getReadBases(); byte[] bases = read.getReadBases();
// BUGBUG: Consider looking at degradation of base quality scores in homopolymer runs to detect when the cycle incremented even though the nucleotide didn't change // BUGBUG: Consider looking at degradation of base quality scores in homopolymer runs to detect when the cycle incremented even though the nucleotide didn't change
@ -106,8 +106,6 @@ public class CycleCovariate implements StandardCovariate {
if( iii >= offset && !BaseUtils.isRegularBase(bases[iii]) ) { iii--; } if( iii >= offset && !BaseUtils.isRegularBase(bases[iii]) ) { iii--; }
} }
} }
return cycle;
} }
//----------------------------- //-----------------------------
@ -120,7 +118,7 @@ public class CycleCovariate implements StandardCovariate {
if( read.getReadNegativeStrandFlag() ) { if( read.getReadNegativeStrandFlag() ) {
pos = read.getReadLength() - (offset + 1); pos = read.getReadLength() - (offset + 1);
} }
return pos / 5; // integer division cycle = pos / 5; // integer division
} }
//----------------------------- //-----------------------------
@ -142,6 +140,13 @@ public class CycleCovariate implements StandardCovariate {
read.getReadGroup().setPlatform( defaultPlatform ); read.getReadGroup().setPlatform( defaultPlatform );
return getValue( read, offset ); // a recursive call return getValue( read, offset ); // a recursive call
} }
// TODO -- Ryan: sanity check me [EB]
// differentiate between first and second of pair
if ( read.getReadPairedFlag() && read.getSecondOfPairFlag() )
cycle *= -1;
return cycle;
} }
// Used to get the covariate's value from input csv file in TableRecalibrationWalker // Used to get the covariate's value from input csv file in TableRecalibrationWalker

22
java/test/org/broadinstitute/sting/gatk/walkers/recalibration/RecalibrationWalkersIntegrationTest.java
View File

@ -16,10 +16,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test @Test
public void testCountCovariates1() { public void testCountCovariates1() {
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", "16f87c9644b27c3c3fe7a963eed45d2d" ); e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12892.SLX.SRP000031.2009_06.selected.bam", "9eddef42ae847f2edd966d3a5b463e50" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "5a4873064e602e1f945f3881c6b4a3e5"); e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "22ee532c7e521d8cbfabedb07673429d");
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "42f78368cc85eb3963329ad48c244e80" ); e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "8b91c48f186c1e44723ac4e047ac553c" );
e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "f97ec61e98db1a580900d9f4985080d0" ); e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "f586fcd8642deae6504d39430b20b713" );
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey(); String bam = entry.getKey();
@ -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", "d7f3e0db5ed9fefc917144a0f937d50d" ); 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/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "1f1770363f381d06e8db9fead03ad7bb"); 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", "563cdb25b5a963121299ad319d5ec2ae" ); 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", "dd8b61060914b75199ca5babc60248fa" ); e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "7dd4c6a3f318a1dccb3f33d08bff953b" );
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey(); String bam = entry.getKey();
@ -80,7 +80,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test @Test
public void testCountCovariatesVCF() { public void testCountCovariatesVCF() {
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.SOLID.bam", "bc0e62dc366f2f6ca70847a832b4aad4"); e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "79e6738031f5a6f993838b33d70716c3");
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey(); String bam = entry.getKey();
@ -108,7 +108,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test @Test
public void testCountCovariatesNoReadGroups() { public void testCountCovariatesNoReadGroups() {
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/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "9d83a1653e076e028fecf4c2575f56e9" ); e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "d6f3ea0cf2129ca5488977f087f1aa25" );
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey(); String bam = entry.getKey();
@ -138,7 +138,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
@Test @Test
public void testTableRecalibratorNoReadGroups() { public void testTableRecalibratorNoReadGroups() {
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/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "8853add9cfd0a8171ca917b1c6452e0a" ); e.put( "/humgen/gsa-scr1/GATK_Data/Validation_Data/NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "c0d5fdd6e07395ae2d7b08431995b30d" );
for ( Map.Entry<String, String> entry : e.entrySet() ) { for ( Map.Entry<String, String> entry : e.entrySet() ) {
String bam = entry.getKey(); String bam = entry.getKey();