As per discussions with Tim we are reverting the previous change regarding PairedReadOrderCovariate. The CycleCovariate now differentiates between first and second of pair by multiplying the cycle by -1. PairedReadOrderCovariate has been removed completely.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2592 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin
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@ -50,7 +50,8 @@ public class CycleCovariate implements StandardCovariate {
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// Initialize any member variables using the command-line arguments passed to the walkers
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public void initialize( final RecalibrationArgumentCollection RAC ) {
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if( RAC.DEFAULT_PLATFORM.equalsIgnoreCase( "ILLUMINA" ) || RAC.DEFAULT_PLATFORM.contains( "454" ) || RAC.DEFAULT_PLATFORM.equalsIgnoreCase( "SOLID" ) ) {
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if( RAC.DEFAULT_PLATFORM.equalsIgnoreCase( "SLX" ) || RAC.DEFAULT_PLATFORM.equalsIgnoreCase( "ILLUMINA" ) ||
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RAC.DEFAULT_PLATFORM.contains( "454" ) || RAC.DEFAULT_PLATFORM.equalsIgnoreCase( "SOLID" ) ) {
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defaultPlatform = RAC.DEFAULT_PLATFORM;
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} else {
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throw new StingException( "The requested default platform (" + RAC.DEFAULT_PLATFORM +") is not a recognized platform. Implemented options are illumina, 454, and solid");
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@ -66,7 +67,8 @@ public class CycleCovariate implements StandardCovariate {
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// ILLUMINA and SOLID
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//-----------------------------
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if( read.getReadGroup().getPlatform().equalsIgnoreCase( "ILLUMINA" ) || read.getReadGroup().getPlatform().equalsIgnoreCase( "SOLID" ) ) {
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if( read.getReadGroup().getPlatform().equalsIgnoreCase( "ILLUMINA" ) || read.getReadGroup().getPlatform().equalsIgnoreCase( "SLX" ) ||
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read.getReadGroup().getPlatform().equalsIgnoreCase( "SOLID" ) ) { // Some bams have "illumina" and others have "SLX"
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cycle = offset + 1;
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if( read.getReadNegativeStrandFlag() ) {
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cycle = read.getReadLength() - offset;
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@ -141,11 +143,13 @@ public class CycleCovariate implements StandardCovariate {
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return getValue( read, offset ); // A recursive call
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}
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// This functionality was moved to PairedReadOrderCovariate
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// Differentiate between first and second of pair
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//if( read.getReadPairedFlag() && read.getSecondOfPairFlag() ) {
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// cycle *= -1;
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//}
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// The sequencing machine cycle keeps incrementing for the second read in a pair. So it is possible for a read group
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// to have an error affecting quality at a particular cycle on only second of pair reads. Therefore the cycle covariate must differentiate
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// between first and second of pair reads.
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if( read.getReadPairedFlag() && read.getSecondOfPairFlag() ) {
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cycle *= -1;
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}
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return cycle;
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}
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@ -1,26 +0,0 @@
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package org.broadinstitute.sting.gatk.walkers.recalibration;
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import net.sf.samtools.SAMRecord;
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/**
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* Created by IntelliJ IDEA.
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* User: chartl
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* Date: Dec 16, 2009
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*/
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public class PairedReadOrderCovariate implements StandardCovariate{
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// Initialize any member variables using the command-line arguments passed to the walkers
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public void initialize ( final RecalibrationArgumentCollection rac ) { /* do nothing */ }
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// Used to pick out the covariate's value from attributes of the read
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public final Comparable getValue( final SAMRecord read, final int offset ) {
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return read.getReadPairedFlag() ? (read.getFirstOfPairFlag() ? "First_Read" : "Second_Read") : "Not_Paired";
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}
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// Used to get the covariate's value from input csv file in TableRecalibrationWalker
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public final Comparable getValue( final String str ) {
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return str;
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}
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}
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@ -57,7 +57,7 @@ public class RecalDataManager {
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private static boolean warnUserNullReadGroup = false;
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private static boolean warnUserNoColorSpace = false;
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public static final String versionString = "v2.2.11"; // Major version, minor version, and build number
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public static final String versionString = "v2.2.12"; // Major version, minor version, and build number
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RecalDataManager() {
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data = new NestedHashMap();
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@ -16,10 +16,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
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@Test
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public void testCountCovariates1() {
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HashMap<String, String> e = new HashMap<String, String>();
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e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "e67a329112061beba0f774844e5f4635" );
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "a626fa8f9c3836ec9764a718c4b6a27f");
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e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "284939b3760a95f51c350c8340b99b31" );
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "c7c28128edf4a54e6ac9e752ebaca697" );
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e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "e5b2d5a2f4283718dae678cbc84be847" );
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "89084b43b824f9e3c5e2afdfe0930542");
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e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "7d6428a76e07ed4b99351aa4df89634d" );
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "6ede6fc840c4e5070a58a919b48e7504" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -37,7 +37,6 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
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" -cov CycleCovariate" +
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" -cov DinucCovariate" +
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" -cov TileCovariate" +
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" -cov PairedReadOrderCovariate" +
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" --solid_recal_mode SET_Q_ZERO" +
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" -recalFile %s",
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1, // just one output file
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@ -50,10 +49,10 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
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@Test
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public void testTableRecalibrator1() {
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HashMap<String, String> e = new HashMap<String, String>();
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e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "c0dbc69726e1827e1eabdc777d8435e2" );
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "b6a1749aa311f5c50097280579c638a3");
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e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "b5bd41672805e15c6a5187c902c1ef9a" );
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "51aeb06db11b66d9e1199ebed9c0562c" );
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e.put( validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.bam", "6c59d291c37d053e0f188b762f3060a5" );
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "e06f1397b9c40f75e96cd3df76730ee0");
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e.put( validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.bam", "7ebdce416b72679e1cf88cc9886a5edc" );
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.allTechs.bam", "48ddc93cae054f9423f3a7ed9f36540e" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -81,7 +80,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
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@Test
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public void testTableRecalibratorMaxQ70() {
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HashMap<String, String> e = new HashMap<String, String>();
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "df4f9bf64cf1a7aa890b28de043cac40" );
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "665711dfb81d67582b28faea24e26160" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -113,7 +112,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
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@Test
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public void testCountCovariatesVCF() {
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HashMap<String, String> e = new HashMap<String, String>();
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "e11048d253a5ca719a373a9dd8e18f40");
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "9b9d21ffb70f15ef2aebad21f3fc05cb");
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -140,7 +139,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
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@Test
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public void testCountCovariatesVCFPlusDBsnp() {
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HashMap<String, String> e = new HashMap<String, String>();
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "33fa86ad0116f727dd6428bb5a2daf30");
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "cc1cc9c1ff184d388d81574fdccc608e");
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -168,7 +167,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
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@Test
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public void testCountCovariatesNoReadGroups() {
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HashMap<String, String> e = new HashMap<String, String>();
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e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "e7031fdf3a88c27ce1b3d5d425860286" );
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e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "a86c64f649b847b7f81ac50a808d3d45" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -197,7 +196,7 @@ public class RecalibrationWalkersIntegrationTest extends WalkerTest {
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@Test
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public void testTableRecalibratorNoReadGroups() {
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HashMap<String, String> e = new HashMap<String, String>();
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e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "de1a08b45250f090f19e6a35d449c50c" );
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e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "32ad300e8c094ed2c1ec6c531180fe70" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -26,7 +26,6 @@
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.PairedReadOrderCovariate</class>
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<!-- Local realignment around indels -->
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<class>org.broadinstitute.sting.gatk.walkers.indels.CleanedReadInjector</class>
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<class>org.broadinstitute.sting.gatk.walkers.indels.IndelIntervalWalker</class>
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@ -66,7 +65,6 @@
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.ReadGroupCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.HomopolymerCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.TileCovariate</class>
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<class>org.broadinstitute.sting.gatk.walkers.recalibration.PairedReadOrderCovariate</class>
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</dependencies>
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</executable>
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<resources>
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