zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added positive/negative strand to the synthetic reads

This commit is contained in:
Mauricio Carneiro 2012-08-15 15:29:55 -04:00
parent 51cb5098e4
commit 2c3dc291c0
3 changed files with 25 additions and 20 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

33
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
View File

@ -263,7 +263,7 @@ public class SlidingWindow {
* @param end the first header index NOT TO add to consensus
* @return a list of consensus reads generated by this call. Empty list if no consensus was generated.
*/
protected List<GATKSAMRecord> addToSyntheticReads(LinkedList<HeaderElement> header, int start, int end) {
protected List<GATKSAMRecord> addToSyntheticReads(LinkedList<HeaderElement> header, int start, int end, boolean isNegativeStrand) {
LinkedList<GATKSAMRecord> reads = new LinkedList<GATKSAMRecord>();
if (start < end) {
ListIterator<HeaderElement> headerElementIterator = header.listIterator(start);
@ -277,22 +277,22 @@ public class SlidingWindow {
reads.addAll(finalizeAndAdd(ConsensusType.FILTERED));
int endOfConsensus = findNextNonConsensusElement(header, start, end);
addToRunningConsensus(header, start, endOfConsensus);
addToRunningConsensus(header, start, endOfConsensus, isNegativeStrand);
if (endOfConsensus <= start)
throw new ReviewedStingException(String.format("next start is <= current start: (%d <= %d)", endOfConsensus, start));
reads.addAll(addToSyntheticReads(header, endOfConsensus, end));
reads.addAll(addToSyntheticReads(header, endOfConsensus, end, isNegativeStrand));
} else if (headerElement.hasFilteredData()) {
reads.addAll(finalizeAndAdd(ConsensusType.CONSENSUS));
int endOfFilteredData = findNextNonFilteredDataElement(header, start, end);
addToFilteredData(header, start, endOfFilteredData);
addToFilteredData(header, start, endOfFilteredData, isNegativeStrand);
if (endOfFilteredData <= start)
throw new ReviewedStingException(String.format("next start is <= current start: (%d <= %d)", endOfFilteredData, start));
reads.addAll(addToSyntheticReads(header, endOfFilteredData, end));
reads.addAll(addToSyntheticReads(header, endOfFilteredData, end, isNegativeStrand));
} else if (headerElement.isEmpty()) {
reads.addAll(finalizeAndAdd(ConsensusType.BOTH));
@ -301,7 +301,7 @@ public class SlidingWindow {
if (endOfEmptyData <= start)
throw new ReviewedStingException(String.format("next start is <= current start: (%d <= %d)", endOfEmptyData, start));
reads.addAll(addToSyntheticReads(header, endOfEmptyData, end));
reads.addAll(addToSyntheticReads(header, endOfEmptyData, end, isNegativeStrand));
} else
throw new ReviewedStingException(String.format("Header Element %d is neither Consensus, Data or Empty. Something is wrong.", start));
@ -414,9 +414,9 @@ public class SlidingWindow {
* @param start the first header index to add to consensus
* @param end the first header index NOT TO add to consensus
*/
private void addToFilteredData(LinkedList<HeaderElement> header, int start, int end) {
private void addToFilteredData(LinkedList<HeaderElement> header, int start, int end, boolean isNegativeStrand) {
if (filteredDataConsensus == null)
filteredDataConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, filteredDataReadName + filteredDataConsensusCounter++, header.get(start).getLocation(), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities);
filteredDataConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, filteredDataReadName + filteredDataConsensusCounter++, header.get(start).getLocation(), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities, isNegativeStrand);
ListIterator<HeaderElement> headerElementIterator = header.listIterator(start);
for (int index = start; index < end; index++) {
@ -443,9 +443,9 @@ public class SlidingWindow {
* @param start the first header index to add to consensus
* @param end the first header index NOT TO add to consensus
*/
private void addToRunningConsensus(LinkedList<HeaderElement> header, int start, int end) {
private void addToRunningConsensus(LinkedList<HeaderElement> header, int start, int end, boolean isNegativeStrand) {
if (runningConsensus == null)
runningConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, consensusReadName + consensusCounter++, header.get(start).getLocation(), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities);
runningConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, consensusReadName + consensusCounter++, header.get(start).getLocation(), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities, isNegativeStrand);
Iterator<HeaderElement> headerElementIterator = header.listIterator(start);
for (int index = start; index < end; index++) {
@ -509,7 +509,8 @@ public class SlidingWindow {
int refStop = windowHeader.get(stop).getLocation();
// Try to compress the variant region
if (canCompress) {
// the "foundEvent" protects us from trying to compress variant regions that are created by insertions
if (canCompress && foundEvent) {
allReads = createPolyploidConsensus(start, stop, nHaplotypes, ((HeaderElement) header[hetRefPosition]).getLocation());
}
@ -545,7 +546,7 @@ public class SlidingWindow {
List<GATKSAMRecord> allReads = compressVariantRegion(start, stop);
List<GATKSAMRecord> result = (downsampleCoverage > 0) ? downsampleVariantRegion(allReads) : allReads;
result.addAll(addToSyntheticReads(windowHeader, 0, start));
result.addAll(addToSyntheticReads(windowHeader, 0, start, false));
result.addAll(finalizeAndAdd(ConsensusType.BOTH));
return result; // finalized reads will be downsampled if necessary
@ -611,7 +612,7 @@ public class SlidingWindow {
finalizedReads = closeVariantRegions(regions, true);
if (!windowHeader.isEmpty()) {
finalizedReads.addAll(addToSyntheticReads(windowHeader, 0, windowHeader.size() - 1));
finalizedReads.addAll(addToSyntheticReads(windowHeader, 0, windowHeader.size() - 1, false));
finalizedReads.addAll(finalizeAndAdd(ConsensusType.BOTH)); // if it ended in running consensus, finish it up
}
@ -668,7 +669,7 @@ public class SlidingWindow {
int refStop = windowHeader.get(stop).getLocation();
List<GATKSAMRecord> toRemove = new LinkedList<GATKSAMRecord>();
for (GATKSAMRecord read : readsInWindow) {
int haplotype = -1;
int haplotype;
// check if the read is either before or inside the variant region
if (read.getSoftStart() <= refStop) {
@ -706,13 +707,13 @@ public class SlidingWindow {
for (LinkedList<HeaderElement> header : headersPosStrand) {
if (header.size() > 0)
hetReads.addAll(addToSyntheticReads(header, 0, header.size()));
hetReads.addAll(addToSyntheticReads(header, 0, header.size(), false));
if (runningConsensus != null)
hetReads.add(finalizeRunningConsensus());
}
for (LinkedList<HeaderElement> header : headersNegStrand) {
if (header.size() > 0)
hetReads.addAll(addToSyntheticReads(header, 0, header.size()));
hetReads.addAll(addToSyntheticReads(header, 0, header.size(), true));
if (runningConsensus != null)
hetReads.add(finalizeRunningConsensus());
}

10
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java
View File

@ -5,9 +5,9 @@ import net.sf.samtools.Cigar;
import net.sf.samtools.CigarElement;
import net.sf.samtools.CigarOperator;
import net.sf.samtools.SAMFileHeader;
import org.broadinstitute.sting.utils.recalibration.EventType;
import org.broadinstitute.sting.utils.MathUtils;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.recalibration.EventType;
import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
@ -46,6 +46,7 @@ public class SyntheticRead {
private String readName;
private Integer refStart;
private boolean hasIndelQualities = false;
private boolean isNegativeStrand = false;
/**
* Full initialization of the running consensus if you have all the information and are ready to
@ -59,7 +60,7 @@ public class SyntheticRead {
* @param refStart the alignment start (reference based)
* @param readTag the reduce reads tag for the synthetic read
*/
public SyntheticRead(SAMFileHeader header, GATKSAMReadGroupRecord readGroupRecord, String contig, int contigIndex, String readName, Integer refStart, String readTag, boolean hasIndelQualities) {
public SyntheticRead(SAMFileHeader header, GATKSAMReadGroupRecord readGroupRecord, String contig, int contigIndex, String readName, Integer refStart, String readTag, boolean hasIndelQualities, boolean isNegativeRead) {
final int initialCapacity = 10000;
bases = new ArrayList<BaseIndex>(initialCapacity);
counts = new ArrayList<Byte>(initialCapacity);
@ -76,9 +77,10 @@ public class SyntheticRead {
this.readName = readName;
this.refStart = refStart;
this.hasIndelQualities = hasIndelQualities;
this.isNegativeStrand = isNegativeRead;
}
public SyntheticRead(List<BaseIndex> bases, List<Byte> counts, List<Byte> quals, List<Byte> insertionQuals, List<Byte> deletionQuals, double mappingQuality, String readTag, SAMFileHeader header, GATKSAMReadGroupRecord readGroupRecord, String contig, int contigIndex, String readName, Integer refStart, boolean hasIndelQualities) {
public SyntheticRead(List<BaseIndex> bases, List<Byte> counts, List<Byte> quals, List<Byte> insertionQuals, List<Byte> deletionQuals, double mappingQuality, String readTag, SAMFileHeader header, GATKSAMReadGroupRecord readGroupRecord, String contig, int contigIndex, String readName, Integer refStart, boolean hasIndelQualities, boolean isNegativeRead) {
this.bases = bases;
this.counts = counts;
this.quals = quals;
@ -93,6 +95,7 @@ public class SyntheticRead {
this.readName = readName;
this.refStart = refStart;
this.hasIndelQualities = hasIndelQualities;
this.isNegativeStrand = isNegativeRead;
}
/**
@ -133,6 +136,7 @@ public class SyntheticRead {
read.setReferenceIndex(contigIndex);
read.setReadPairedFlag(false);
read.setReadUnmappedFlag(false);
read.setReadNegativeStrandFlag(isNegativeStrand);
read.setCigar(buildCigar()); // the alignment start may change while building the cigar (leading deletions)
read.setAlignmentStart(refStart);
read.setReadName(readName);

2
protected/java/test/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticReadUnitTest.java
View File

@ -35,7 +35,7 @@ public void testBaseCounts() {
new TestRead(bases, quals, new Byte[] {1, 127, 51, 126}, new byte [] {1, 126, 50, 125})};
for (TestRead testRead : testReads) {
SyntheticRead syntheticRead = new SyntheticRead(Arrays.asList(testRead.getBases()), Arrays.asList(testRead.getCounts()), Arrays.asList(testRead.getQuals()), Arrays.asList(testRead.getInsQuals()), Arrays.asList(testRead.getDelQuals()), artificialMappingQuality, GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, artificialSAMHeader, artificialGATKRG, artificialContig, artificialContigIndex, artificialReadName, artificialRefStart, false);
SyntheticRead syntheticRead = new SyntheticRead(Arrays.asList(testRead.getBases()), Arrays.asList(testRead.getCounts()), Arrays.asList(testRead.getQuals()), Arrays.asList(testRead.getInsQuals()), Arrays.asList(testRead.getDelQuals()), artificialMappingQuality, GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, artificialSAMHeader, artificialGATKRG, artificialContig, artificialContigIndex, artificialReadName, artificialRefStart, false, false);
Assert.assertEquals(syntheticRead.convertBaseCounts(), testRead.getExpectedCounts());
}
}