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Fixing conflicts 

Conflicts:
	public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
This commit is contained in:
Mauricio Carneiro 2011-10-03 19:07:59 -07:00
parent bf6a3a6532 c3eff7451a
commit 3837aa45b4
10 changed files with 87 additions and 92 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
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@ -32,16 +32,11 @@ import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.utils.Haplotype;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.exceptions.UserException;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import java.io.File;
import java.io.FileWriter;
import java.io.PrintStream;
import java.util.Arrays;
import java.util.HashMap;
import java.util.LinkedHashMap;
@ -415,10 +410,6 @@ public class PairHMMIndelErrorModel {
if (read == null)
continue;
if ( isReduced ) {
read = ReadUtils.reducedReadWithReducedQuals(read);
}
if(ReadUtils.is454Read(read)) {
continue;
}

13
public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
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@ -36,12 +36,8 @@ import org.broadinstitute.sting.gatk.datasources.reference.ReferenceDataSource;
import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
import org.broadinstitute.sting.gatk.filters.Platform454Filter;
import org.broadinstitute.sting.gatk.filters.PlatformUnitFilter;
import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
import org.broadinstitute.sting.gatk.refdata.SeekableRODIterator;
import org.broadinstitute.sting.utils.codecs.refseq.Transcript;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackBuilder;
import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
@ -51,6 +47,9 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocSortedSet;
import org.broadinstitute.sting.utils.SampleUtils;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
import org.broadinstitute.sting.utils.codecs.refseq.Transcript;
import org.broadinstitute.sting.utils.codecs.vcf.*;
import org.broadinstitute.sting.utils.collections.CircularArray;
import org.broadinstitute.sting.utils.collections.PrimitivePair;
@ -265,7 +264,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
Set<VCFHeaderLine> headerInfo = new HashSet<VCFHeaderLine>();
// first, the basic info
headerInfo.add(new VCFHeaderLine("source", "IndelGenotyperV2"));
headerInfo.add(new VCFHeaderLine("source", "SomaticIndelDetector"));
headerInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
// FORMAT and INFO fields
@ -283,10 +282,10 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
args.addAll(getToolkit().getFilters());
Map<String,String> commandLineArgs = getToolkit().getApproximateCommandLineArguments(args);
for ( Map.Entry<String, String> commandLineArg : commandLineArgs.entrySet() )
headerInfo.add(new VCFHeaderLine(String.format("IGv2_%s", commandLineArg.getKey()), commandLineArg.getValue()));
headerInfo.add(new VCFHeaderLine(String.format("SID_%s", commandLineArg.getKey()), commandLineArg.getValue()));
// also, the list of input bams
for ( String fileName : getToolkit().getArguments().samFiles )
headerInfo.add(new VCFHeaderLine("IGv2_bam_file_used", fileName));
headerInfo.add(new VCFHeaderLine("SID_bam_file_used", fileName));
return headerInfo;
}

6
public/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/TableRecalibrationWalker.java
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@ -170,9 +170,9 @@ public class TableRecalibrationWalker extends ReadWalker<SAMRecord, SAMFileWrite
/////////////////////////////
private RecalDataManager dataManager; // Holds the data HashMap, mostly used by TableRecalibrationWalker to create collapsed data hashmaps
private final ArrayList<Covariate> requestedCovariates = new ArrayList<Covariate>(); // List of covariates to be used in this calculation
private static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
private static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
private static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
public static final Pattern COMMENT_PATTERN = Pattern.compile("^#.*");
public static final Pattern OLD_RECALIBRATOR_HEADER = Pattern.compile("^rg,.*");
public static final Pattern COVARIATE_PATTERN = Pattern.compile("^ReadGroup,QualityScore,.*");
public static final String EOF_MARKER = "EOF";
private long numReadsWithMalformedColorSpace = 0;

7
public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java
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@ -4,7 +4,6 @@ import com.google.java.contract.Requires;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.sam.ReadUtils;
@ -94,6 +93,12 @@ public class ReadClipper {
if (left == right)
return new SAMRecord(read.getHeader());
SAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);
// after clipping one tail, it is possible that the consequent hard clipping of adjacent deletions
// make the left cut index no longer part of the read. In that case, clip the read entirely.
if (left > leftTailRead.getAlignmentEnd())
return new SAMRecord(read.getHeader());
ReadClipper clipper = new ReadClipper(leftTailRead);
return clipper.hardClipByReferenceCoordinatesLeftTail(left);
}

28
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
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@ -36,6 +36,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
// for ParsingUtils.split
protected String[] GTValueArray = new String[100];
protected String[] genotypeKeyArray = new String[100];
protected String[] infoFieldArray = new String[1000];
protected String[] infoValueArray = new String[1000];
// for performance testing purposes
@ -351,23 +352,28 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec,
if ( infoField.indexOf("\t") != -1 || infoField.indexOf(" ") != -1 )
generateException("The VCF specification does not allow for whitespace in the INFO field");
int infoValueSplitSize = ParsingUtils.split(infoField, infoValueArray, VCFConstants.INFO_FIELD_SEPARATOR_CHAR);
for (int i = 0; i < infoValueSplitSize; i++) {
int infoFieldSplitSize = ParsingUtils.split(infoField, infoFieldArray, VCFConstants.INFO_FIELD_SEPARATOR_CHAR, false);
for (int i = 0; i < infoFieldSplitSize; i++) {
String key;
Object value;
int eqI = infoValueArray[i].indexOf("=");
int eqI = infoFieldArray[i].indexOf("=");
if ( eqI != -1 ) {
key = infoValueArray[i].substring(0, eqI);
String str = infoValueArray[i].substring(eqI+1, infoValueArray[i].length());
key = infoFieldArray[i].substring(0, eqI);
String str = infoFieldArray[i].substring(eqI+1);
// lets see if the string contains a , separator
if ( str.contains(",") )
value = Arrays.asList(str.split(","));
else
value = str;
// split on the INFO field separator
int infoValueSplitSize = ParsingUtils.split(str, infoValueArray, VCFConstants.INFO_FIELD_ARRAY_SEPARATOR_CHAR, false);
if ( infoValueSplitSize == 1 ) {
value = infoValueArray[0];
} else {
ArrayList<String> valueList = new ArrayList<String>(infoValueSplitSize);
for ( int j = 0; j < infoValueSplitSize; j++ )
valueList.add(infoValueArray[j]);
value = valueList;
}
} else {
key = infoValueArray[i];
key = infoFieldArray[i];
value = true;
}

1
public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
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@ -71,6 +71,7 @@ public final class VCFConstants {
public static final char FIELD_SEPARATOR_CHAR = '\t';
public static final String FILTER_CODE_SEPARATOR = ";";
public static final String INFO_FIELD_ARRAY_SEPARATOR = ",";
public static final char INFO_FIELD_ARRAY_SEPARATOR_CHAR = ',';
public static final String ID_FIELD_SEPARATOR = ";";
public static final String INFO_FIELD_SEPARATOR = ";";
public static final char INFO_FIELD_SEPARATOR_CHAR = ';';

6
public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
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@ -87,11 +87,11 @@ public class PileupElement {
public int getReducedCount() {
if ( ! isReducedRead() ) throw new IllegalArgumentException("Cannot get reduced count for non-reduced read " + getRead().getReadName());
return (int)getQual();
return ReadUtils.getReducedCount(getRead(), offset);
}
public byte getReducedQual() {
return (byte)(int)ReadUtils.getReducedReadQualityTagValue(getRead());
if ( ! isReducedRead() ) throw new IllegalArgumentException("Cannot get reduced qual for non-reduced read " + getRead().getReadName());
return ReadUtils.getReducedQual(getRead(), offset);
}
}

48
public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java
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@ -52,27 +52,37 @@ public class ReadUtils {
// ----------------------------------------------------------------------------------------------------
public static final String REDUCED_READ_QUALITY_TAG = "RQ";
public static final String REDUCED_READ_CONSENSUS_COUNTS_TAG = "CC";
public final static Integer getReducedReadQualityTagValue(final SAMRecord read) {
return read.getIntegerAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
public final static byte[] getReducedReadQualityTagValue(final SAMRecord read) {
return read.getByteArrayAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG);
}
public final static boolean isReducedRead(final SAMRecord read) {
return getReducedReadQualityTagValue(read) != null;
}
public final static byte getReducedQual(final SAMRecord read, final int i) {
return read.getBaseQualities()[i];
}
public final static byte getReducedCount(final SAMRecord read, final int i) {
return getReducedReadQualityTagValue(read)[i];
}
public final static SAMRecord reducedReadWithReducedQuals(final SAMRecord read) {
if ( ! isReducedRead(read) ) throw new IllegalArgumentException("read must be a reduced read");
try {
SAMRecord newRead = (SAMRecord)read.clone();
byte reducedQual = (byte)(int)getReducedReadQualityTagValue(read);
byte[] newQuals = new byte[read.getBaseQualities().length];
Arrays.fill(newQuals, reducedQual);
newRead.setBaseQualities(newQuals);
return newRead;
} catch ( CloneNotSupportedException e ) {
throw new ReviewedStingException("SAMRecord no longer supports clone", e);
}
return read;
// try {
// SAMRecord newRead = (SAMRecord)read.clone();
// byte reducedQual = (byte)(int)getReducedReadQualityTagValue(read);
// byte[] newQuals = new byte[read.getBaseQualities().length];
// Arrays.fill(newQuals, reducedQual);
// newRead.setBaseQualities(newQuals);
// return newRead;
// } catch ( CloneNotSupportedException e ) {
// throw new ReviewedStingException("SAMRecord no longer supports clone", e);
// }
}
// ----------------------------------------------------------------------------------------------------
@ -878,9 +888,20 @@ public class ReadUtils {
if (endsWithinCigar)
fallsInsideDeletion = cigarElement.getOperator() == CigarOperator.DELETION;
// if we end outside the current cigar element, we need to check if the next element is a deletion.
// if we end outside the current cigar element, we need to check if the next element is an insertion or deletion.
else {
nextCigarElement = cigarElementIterator.next();
// if it's an insertion, we need to clip the whole insertion before looking at the next element
if (nextCigarElement.getOperator() == CigarOperator.INSERTION) {
readBases += nextCigarElement.getLength();
if (!cigarElementIterator.hasNext())
throw new ReviewedStingException("Reference coordinate corresponds to a non-existent base in the read. This should never happen -- call Mauricio");
nextCigarElement = cigarElementIterator.next();
}
// if it's a deletion, we will pass the information on to be handled downstream.
fallsInsideDeletion = nextCigarElement.getOperator() == CigarOperator.DELETION;
}
@ -965,4 +986,5 @@ public class ReadUtils {
AlignmentStartComparator comp = new AlignmentStartComparator();
return comp.compare(read1, read2);
}
}

29
public/java/test/org/broadinstitute/sting/utils/ReadUtilsUnitTest.java
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@ -7,7 +7,6 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.broadinstitute.sting.utils.sam.ReadUtils;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
@ -16,7 +15,7 @@ public class ReadUtilsUnitTest extends BaseTest {
SAMRecord read, reducedRead;
final static String BASES = "ACTG";
final static String QUALS = "!+5?";
final private static int REDUCED_READ_QUAL = 20;
final private static byte[] REDUCED_READ_COUNTS = new byte[]{10, 20, 30, 40};
@BeforeTest
public void init() {
@ -29,7 +28,7 @@ public class ReadUtilsUnitTest extends BaseTest {
reducedRead = ArtificialSAMUtils.createArtificialRead(header, "reducedRead", 0, 1, BASES.length());
reducedRead.setReadBases(BASES.getBytes());
reducedRead.setBaseQualityString(QUALS);
reducedRead.setAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG, REDUCED_READ_QUAL);
reducedRead.setAttribute(ReadUtils.REDUCED_READ_QUALITY_TAG, REDUCED_READ_COUNTS);
}
private void testReadBasesAndQuals(SAMRecord read, int expectedStart, int expectedStop) {
@ -52,21 +51,10 @@ public class ReadUtilsUnitTest extends BaseTest {
Assert.assertEquals(ReadUtils.getReducedReadQualityTagValue(read), null, "No reduced read tag in normal read");
Assert.assertTrue(ReadUtils.isReducedRead(reducedRead), "isReducedRead is true for reduced read");
Assert.assertEquals((int) ReadUtils.getReducedReadQualityTagValue(reducedRead), REDUCED_READ_QUAL, "Reduced read tag is set to expected value");
}
@Test
public void testreducedReadWithReducedQualsWithReducedRead() {
SAMRecord replacedRead = ReadUtils.reducedReadWithReducedQuals(reducedRead);
Assert.assertEquals(replacedRead.getReadBases(), reducedRead.getReadBases());
Assert.assertEquals(replacedRead.getBaseQualities().length, reducedRead.getBaseQualities().length);
for ( int i = 0; i < replacedRead.getBaseQualities().length; i++)
Assert.assertEquals(replacedRead.getBaseQualities()[i], REDUCED_READ_QUAL);
}
@Test(expectedExceptions = IllegalArgumentException.class)
public void testreducedReadWithReducedQualsWithNormalRead() {
ReadUtils.reducedReadWithReducedQuals(read);
for ( int i = 0; i < reducedRead.getReadLength(); i++) {
Assert.assertEquals(ReadUtils.getReducedQual(reducedRead, i), read.getBaseQualities()[i], "Reduced read quality not set to the expected value at " + i);
Assert.assertEquals(ReadUtils.getReducedCount(reducedRead, i), REDUCED_READ_COUNTS[i], "Reduced read count not set to the expected value at " + i);
}
}
@Test
@ -77,8 +65,7 @@ public class ReadUtilsUnitTest extends BaseTest {
Assert.assertFalse(readp.isReducedRead());
Assert.assertTrue(reducedreadp.isReducedRead());
Assert.assertEquals(reducedreadp.getReducedCount(), 0);
Assert.assertEquals(reducedreadp.getReducedQual(), REDUCED_READ_QUAL);
Assert.assertEquals(reducedreadp.getReducedCount(), REDUCED_READ_COUNTS[0]);
Assert.assertEquals(reducedreadp.getReducedQual(), readp.getQual());
}
}

32
public/java/test/org/broadinstitute/sting/utils/clipreads/ReadClipperUnitTest.java
View File

@ -25,16 +25,14 @@
package org.broadinstitute.sting.utils.clipreads;
import net.sf.samtools.*;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.BaseTest;
import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
import org.testng.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import java.util.LinkedList;
import java.util.List;
/**
* Created by IntelliJ IDEA.
* User: roger
@ -62,21 +60,7 @@ public class ReadClipperUnitTest extends BaseTest {
readClipper = new ReadClipper(read);
}
private void testHardClipCigarByReadCoordinate( SAMRecord read, String inputCigar, String expectedCigar, int expectedStart, int expectedStop) {
read.setCigar(TextCigarCodec.getSingleton().decode(inputCigar) );
SAMRecord clipped = readClipper.hardClipByReadCoordinates(expectedStart,expectedStop);
Assert.assertEquals(clipped.getCigarString(), expectedCigar, "Clipped Cigar string is different than expected");
}
/*
private void testReadBasesAndQuals(SAMRecord read, int expectedStart, int expectedStop) {
SAMRecord clipped = ReadUtils.hardClipBases(read, expectedStart, expectedStop - 1, null);
String expectedBases = BASES.substring(expectedStart, expectedStop);
String expectedQuals = QUALS.substring(expectedStart, expectedStop);
Assert.assertEquals(clipped.getReadBases(), expectedBases.getBytes(), "Clipped bases not those expected");
Assert.assertEquals(clipped.getBaseQualityString(), expectedQuals, "Clipped quals not those expected");
}
*/
@Test
@Test ( enabled = false )
public void testHardClipBothEndsByReferenceCoordinates() {
logger.warn("Executing testHardClipBothEndsByReferenceCoordinates");
@ -90,7 +74,7 @@ public class ReadClipperUnitTest extends BaseTest {
}
@Test
@Test ( enabled = false )
public void testHardClipByReadCoordinates() {
logger.warn("Executing testHardClipByReadCoordinates");
@ -123,7 +107,7 @@ public class ReadClipperUnitTest extends BaseTest {
}
@Test
@Test ( enabled = false )
public void testHardClipByReferenceCoordinates() {
logger.warn("Executing testHardClipByReferenceCoordinates");
@ -156,7 +140,7 @@ public class ReadClipperUnitTest extends BaseTest {
}
@Test
@Test ( enabled = false )
public void testHardClipByReferenceCoordinatesLeftTail() {
logger.warn("Executing testHardClipByReferenceCoordinatesLeftTail");
@ -177,7 +161,7 @@ public class ReadClipperUnitTest extends BaseTest {
}
@Test
@Test ( enabled = false )
public void testHardClipByReferenceCoordinatesRightTail() {
logger.warn("Executing testHardClipByReferenceCoordinatesRightTail");
@ -198,7 +182,7 @@ public class ReadClipperUnitTest extends BaseTest {
}
@Test
@Test ( enabled = false )
public void testHardClipLowQualEnds() {
logger.warn("Executing testHardClipByReferenceCoordinates");