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Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/stable

This commit is contained in:
Ryan Poplin 2012-08-30 09:19:35 -04:00
parent 5f8574bd15 150a969279
commit eb63221875
6 changed files with 39 additions and 75 deletions
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1
public/java/src/org/broadinstitute/sting/gatk/iterators/LocusIteratorByState.java
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@ -318,6 +318,7 @@ public class LocusIteratorByState extends LocusIterator {
continue;
if (op == CigarOperator.D) {
// TODO -- LIBS is totally busted for deletions so that reads with Ds right before Is in their CIGAR are broken; must fix
if (readInfo.includeReadsWithDeletionAtLoci()) { // only add deletions to the pileup if we are authorized to do so
pile.add(new PileupElement(read, readOffset, true, isBeforeDeletion, isAfterDeletion, isBeforeInsertion, isAfterInsertion, isNextToSoftClip, null, nextOp == CigarOperator.D ? nextElementLength : -1));
size++;

6
public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
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@ -88,7 +88,11 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
for ( PileupElement p : pileup ) {
if ( p.isBeforeInsertion() ) {
final Allele insertion = Allele.create((char)refBase + p.getEventBases(), false);
final String eventBases = p.getEventBases();
if ( eventBases == null )
continue;
final Allele insertion = Allele.create((char)refBase + eventBases, false);
if ( alleleCounts.containsKey(insertion) ) {
alleleCounts.put(insertion, alleleCounts.get(insertion)+1);
}

4
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
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@ -1181,10 +1181,10 @@ public class SomaticIndelDetector extends ReadWalker<Integer,Integer> {
if ( event_length == 0 ) { // insertion
l.add( Allele.create(referencePaddingBase,true) );
l.add( Allele.create(referencePaddingBase + call.getVariant().getBases(), false ));
l.add( Allele.create((char)referencePaddingBase + new String(call.getVariant().getBases()), false ));
} else { //deletion:
l.add( Allele.create(referencePaddingBase + call.getVariant().getBases(), true ));
l.add( Allele.create((char)referencePaddingBase + new String(call.getVariant().getBases()), true ));
l.add( Allele.create(referencePaddingBase,false) );
}
}

15
public/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
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@ -25,12 +25,14 @@
package org.broadinstitute.sting.utils.classloader;
import org.broadinstitute.sting.utils.Utils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.exceptions.StingException;
import org.reflections.util.ClasspathHelper;
import java.io.File;
import java.io.IOException;
import java.lang.annotation.Annotation;
import java.lang.reflect.*;
import java.net.URL;
import java.util.*;
@ -234,4 +236,17 @@ public class JVMUtils {
} else
throw new ReviewedStingException("BUG: could not find generic type on class " + t);
}
/**
* Returns a comma-separated list of the names of the interfaces implemented by this class
*
* @param covClass
* @return
*/
public static String classInterfaces(final Class covClass) {
final List<String> interfaces = new ArrayList<String>();
for ( final Class interfaceClass : covClass.getInterfaces() )
interfaces.add(interfaceClass.getSimpleName());
return Utils.join(", ", interfaces);
}
}

25
public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
View File

@ -29,6 +29,7 @@ import org.apache.log4j.Logger;
import org.broadinstitute.sting.gatk.report.GATKReport;
import org.broadinstitute.sting.gatk.report.GATKReportTable;
import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.classloader.JVMUtils;
import org.broadinstitute.sting.utils.recalibration.covariates.*;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.R.RScriptExecutor;
@ -117,6 +118,12 @@ public class RecalUtils {
if (argumentCollection.COVARIATES != null) { // parse the -cov arguments that were provided, skipping over the ones already specified
for (String requestedCovariateString : argumentCollection.COVARIATES) {
// help the transition from BQSR v1 to BQSR v2
if ( requestedCovariateString.equals("DinucCovariate") )
throw new UserException.CommandLineException("DinucCovariate has been retired. Please use its successor covariate " +
"ContextCovariate instead, which includes the 2 bp (dinuc) substitution model of the retired DinucCovariate " +
"as well as an indel context to model the indel error rates");
boolean foundClass = false;
for (Class<? extends Covariate> covClass : covariateClasses) {
if (requestedCovariateString.equalsIgnoreCase(covClass.getSimpleName())) { // -cov argument matches the class name for an implementing class
@ -178,18 +185,18 @@ public class RecalUtils {
return dest;
}
public static void listAvailableCovariates(Logger logger) {
// Get a list of all available covariates
final List<Class<? extends Covariate>> covariateClasses = new PluginManager<Covariate>(Covariate.class).getPlugins();
// Print and exit if that's what was requested
/**
* Print a list of all available covariates to logger as info
*
* @param logger
*/
public static void listAvailableCovariates(final Logger logger) {
logger.info("Available covariates:");
for (Class<?> covClass : covariateClasses)
logger.info(covClass.getSimpleName());
logger.info("");
for (final Class<? extends Covariate> covClass : new PluginManager<Covariate>(Covariate.class).getPlugins()) {
logger.info(String.format("\t%30s\t%s", covClass.getSimpleName(), JVMUtils.classInterfaces(covClass)));
}
}
public enum SOLID_RECAL_MODE {
/**
* Treat reference inserted bases as reference matching bases. Very unsafe!

63
public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/BinaryTagCovariate.java
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@ -1,63 +0,0 @@
package org.broadinstitute.sting.utils.recalibration.covariates;
import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
/**
* Binary covariate allows BQSR to recalibrate based on a binary covariate in the BAM file. This covariate should assume values of 1 and 0.
*
* @author Mauricio Carneiro
* @since 7/6/12
*/
public class BinaryTagCovariate implements ExperimentalCovariate {
private String tag;
@Override
public void initialize(RecalibrationArgumentCollection RAC) {
tag = RAC.BINARY_TAG_NAME;
}
@Override
public void recordValues(GATKSAMRecord read, ReadCovariates values) {
final Object tagObject = read.getAttribute(tag);
byte[] binaryTag;
if (tagObject instanceof byte[])
binaryTag = (byte[]) tagObject;
else if (tagObject instanceof String) {
int readLength = ((String) tagObject).length();
binaryTag = new byte[readLength];
for (int i = 0; i<readLength; i++)
binaryTag[i] = Byte.decode(((String) tagObject).substring(i, i+1));
}
else
throw new UserException("Binary tag is not a byte array (fast) or a string (slow). Type not supported");
for (int i = 0; i < read.getReadLength(); i++) {
values.addCovariate((int) binaryTag[i], (int) binaryTag[i], (int) binaryTag[i], i);
}
}
@Override
public Object getValue(String str) {
return Integer.decode(str);
}
@Override
public String formatKey(int key) {
return String.format("%d", key);
}
@Override
public int keyFromValue(Object value) {
return Integer.decode((String) value);
}
@Override
public int maximumKeyValue() {
return 1;
}
}