PairedReadOrderCovariate is now a standard covariate and because of this CycleCovariate no longer multiplies by negative one for second of pair reads. Added PairedReadOrderCovariate to some of the integration tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2574 348d0f76-0448-11de-a6fe-93d51630548a
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@ -39,7 +39,7 @@ import net.sf.samtools.SAMRecord;
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* For Solexa the cycle is simply the position in the read (counting backwards if it is a negative strand read)
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* For 454 the cycle is the TACG flow cycle, that is, each flow grabs all the TACG's in order in a single cycle
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* For example, for the read: AAACCCCGAAATTTTTACTG
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* the cycle would be 00000000111222222233
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* the cycle would be 11111111222333333344
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* For SOLiD the cycle is a more complicated mixture of ligation cycle and primer round
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*/
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@ -82,7 +82,7 @@ public class CycleCovariate implements StandardCovariate {
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// 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
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// For example, AAAAAAA was probably read in two flow cycles but here we count it as one
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if( !read.getReadNegativeStrandFlag() ) { // forward direction
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if( !read.getReadNegativeStrandFlag() ) { // Forward direction
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int iii = 0;
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while( iii <= offset )
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{
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@ -94,7 +94,7 @@ public class CycleCovariate implements StandardCovariate {
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if( iii <= offset && !BaseUtils.isRegularBase(bases[iii]) ) { iii++; }
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}
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} else { // negative direction
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} else { // Negative direction
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int iii = bases.length-1;
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while( iii >= offset )
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{
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@ -141,10 +141,11 @@ 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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//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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@ -6,17 +6,19 @@ import net.sf.samtools.SAMRecord;
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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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* Time: 3:22:19 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class PairedReadOrderCovariate implements ExperimentalCovariate{
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public void initialize (final RecalibrationArgumentCollection rac ) { /* do nothing */ }
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public class PairedReadOrderCovariate implements StandardCovariate{
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public final Comparable getValue(final SAMRecord read, final int offset) {
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return read.getReadPairedFlag() ? "Not_Paired" : read.getMateUnmappedFlag() ? "Mate_Unmapped" : read.getFirstOfPairFlag() ? "First_Read" : "Second_Read";
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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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@ -123,7 +123,7 @@ public class RecalDataManager {
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for( int iii = 0; iii < dataCollapsedByCovariate.size(); iii++ ) {
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covariateCollapsedKey[0] = key[0]; // Make a new key with the read group ...
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covariateCollapsedKey[1] = key[1]; // and quality score ...
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Object theCovariateElement = key[iii + 2]; // and the given covariate
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final Object theCovariateElement = key[iii + 2]; // and the given covariate
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if( theCovariateElement != null ) {
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covariateCollapsedKey[2] = theCovariateElement;
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collapsedDatum = (RecalDatum) dataCollapsedByCovariate.get(iii).get( covariateCollapsedKey );
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@ -202,7 +202,7 @@ public class RecalDataManager {
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// Check if we need to use the original quality scores instead
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if( RAC.USE_ORIGINAL_QUALS ) {
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Object attr = read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG);
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final Object attr = read.getAttribute(RecalDataManager.ORIGINAL_QUAL_ATTRIBUTE_TAG);
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if( attr != null ) {
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if( attr instanceof String ) {
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read.setBaseQualities( QualityUtils.fastqToPhred((String)attr) );
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@ -229,7 +229,7 @@ public class RecalDataManager {
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}
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if( RAC.FORCE_READ_GROUP != null && !readGroup.getReadGroupId().equals(RAC.FORCE_READ_GROUP) ) { // Collapse all the read groups into a single common String provided by the user
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String oldPlatform = readGroup.getPlatform();
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final String oldPlatform = readGroup.getPlatform();
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readGroup = new SAMReadGroupRecord( RAC.FORCE_READ_GROUP );
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readGroup.setPlatform( oldPlatform );
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((GATKSAMRecord)read).setReadGroup( readGroup );
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@ -252,7 +252,7 @@ public class RecalDataManager {
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// If this is a SOLID read then we have to check if the color space is inconsistent. This is our only sign that SOLID has inserted the reference base
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if( read.getReadGroup().getPlatform().equalsIgnoreCase("SOLID") ) {
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if( read.getAttribute(RecalDataManager.COLOR_SPACE_INCONSISTENCY_TAG) == null ) { // Haven't calculated the inconsistency array yet for this read
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Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG);
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final Object attr = read.getAttribute(RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG);
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if( attr != null ) {
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char[] colorSpace;
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if( attr instanceof String ) {
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@ -309,7 +309,7 @@ public class RecalDataManager {
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// Loop over the read and calculate first the infered bases from the color and then check if it is consistent with the read
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byte[] readBases = read.getReadBases();
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byte[] colorImpliedBases = readBases.clone();
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final byte[] colorImpliedBases = readBases.clone();
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char[] refBasesDirRead = refBases;
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if( read.getReadNegativeStrandFlag() ) {
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readBases = BaseUtils.simpleReverseComplement( read.getReadBases() );
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@ -489,7 +489,7 @@ public class RecalDataManager {
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return inconsistency[offset] != 0;
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}
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// This block of code is if you want to check both the offset and the next base for color space inconsistency
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// This block of code is for if you want to check both the offset and the next base for color space inconsistency
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//if( read.getReadNegativeStrandFlag() ) { // Negative direction
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// if( offset == 0 ) {
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// return inconsistency[0] != 0;
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@ -503,6 +503,7 @@ public class RecalDataManager {
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// return (inconsistency[offset] != 0) || (inconsistency[offset + 1] != 0);
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// }
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//}
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} else {
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return false;
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}
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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", "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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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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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -37,6 +37,7 @@ 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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@ -49,10 +50,10 @@ 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", "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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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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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -80,7 +81,7 @@ 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", "665711dfb81d67582b28faea24e26160" );
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "df4f9bf64cf1a7aa890b28de043cac40" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -109,7 +110,7 @@ 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", "9b9d21ffb70f15ef2aebad21f3fc05cb");
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "e11048d253a5ca719a373a9dd8e18f40");
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -136,7 +137,7 @@ 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", "cc1cc9c1ff184d388d81574fdccc608e");
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e.put( validationDataLocation + "NA12878.1kg.p2.chr1_10mb_11_mb.SOLID.bam", "33fa86ad0116f727dd6428bb5a2daf30");
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -164,7 +165,7 @@ 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", "a86c64f649b847b7f81ac50a808d3d45" );
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e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "e7031fdf3a88c27ce1b3d5d425860286" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -193,7 +194,7 @@ 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", "32ad300e8c094ed2c1ec6c531180fe70" );
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e.put( validationDataLocation + "NA12762.SOLID.SRP000031.2009_07.chr1.10_20mb.bam", "de1a08b45250f090f19e6a35d449c50c" );
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for ( Map.Entry<String, String> entry : e.entrySet() ) {
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String bam = entry.getKey();
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@ -26,6 +26,7 @@
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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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@ -65,6 +66,7 @@
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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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