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RR bug: when the last base in the window around the polyploid consensus is filtered (low quality), the filtered consensus is not flushed and subsequent filtered bases (but importantly not contiguous to this one) are just added to this position. In other words, bases were being added to the wrong genomic positions. Fixed.

This commit is contained in:
Eric Banks 2012-10-07 10:52:01 -04:00
parent 36a26a7da6
commit 08ac80c080
2 changed files with 23 additions and 10 deletions
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19
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SlidingWindow.java
View File

@ -291,7 +291,7 @@ public class SlidingWindow {
reads.addAll(finalizeAndAdd(ConsensusType.CONSENSUS));
int endOfFilteredData = findNextNonFilteredDataElement(header, start, end);
addToFilteredData(header, start, endOfFilteredData, isNegativeStrand);
reads.addAll(addToFilteredData(header, start, endOfFilteredData, isNegativeStrand));
if (endOfFilteredData <= start)
throw new ReviewedStingException(String.format("next start is <= current start: (%d <= %d)", endOfFilteredData, start));
@ -418,7 +418,9 @@ 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, boolean isNegativeStrand) {
private List<GATKSAMRecord> addToFilteredData(LinkedList<HeaderElement> header, int start, int end, boolean isNegativeStrand) {
List<GATKSAMRecord> result = new ArrayList<GATKSAMRecord>(0);
if (filteredDataConsensus == null)
filteredDataConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, filteredDataReadName + filteredDataConsensusCounter++, header.get(start).getLocation(), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities, isNegativeStrand);
@ -434,8 +436,15 @@ public class SlidingWindow {
if (!headerElement.hasFilteredData())
throw new ReviewedStingException("No filtered data in " + index);
if ( filteredDataConsensus.getRefStart() + filteredDataConsensus.size() != headerElement.getLocation() ) {
result.add(finalizeFilteredDataConsensus());
filteredDataConsensus = new SyntheticRead(samHeader, readGroupAttribute, contig, contigIndex, filteredDataReadName + filteredDataConsensusCounter++, headerElement.getLocation(), GATKSAMRecord.REDUCED_READ_CONSENSUS_TAG, hasIndelQualities, isNegativeStrand);
}
genericAddBaseToConsensus(filteredDataConsensus, headerElement.getFilteredBaseCounts(), headerElement.getRMS());
}
return result;
}
/**
@ -512,9 +521,6 @@ public class SlidingWindow {
}
}
int refStart = windowHeader.get(start).getLocation();
int refStop = windowHeader.get(stop).getLocation();
// Try to compress the variant region
// the "foundEvent" protects us from trying to compress variant regions that are created by insertions
if (canCompress && foundEvent) {
@ -524,6 +530,9 @@ public class SlidingWindow {
// Return all reads that overlap the variant region and remove them from the window header entirely
// also remove all reads preceding the variant region (since they will be output as consensus right after compression
else {
final int refStart = windowHeader.get(start).getLocation();
final int refStop = windowHeader.get(stop).getLocation();
LinkedList<GATKSAMRecord> toRemove = new LinkedList<GATKSAMRecord>();
for (GATKSAMRecord read : readsInWindow) {
if (read.getSoftStart() <= refStop) {

14
protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/SyntheticRead.java
View File

@ -44,7 +44,7 @@ public class SyntheticRead {
private String contig;
private int contigIndex;
private String readName;
private Integer refStart;
private int refStart;
private boolean hasIndelQualities = false;
private boolean isNegativeStrand = false;
@ -60,7 +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, boolean isNegativeRead) {
public SyntheticRead(SAMFileHeader header, GATKSAMReadGroupRecord readGroupRecord, String contig, int contigIndex, String readName, int refStart, String readTag, boolean hasIndelQualities, boolean isNegativeRead) {
final int initialCapacity = 10000;
bases = new ArrayList<BaseIndex>(initialCapacity);
counts = new ArrayList<Byte>(initialCapacity);
@ -80,7 +80,7 @@ public class SyntheticRead {
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, boolean 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, int refStart, boolean hasIndelQualities, boolean isNegativeRead) {
this.bases = bases;
this.counts = counts;
this.quals = quals;
@ -115,11 +115,15 @@ public class SyntheticRead {
this.mappingQuality += mappingQuality;
}
public BaseIndex getBase(int readCoordinate) {
public BaseIndex getBase(final int readCoordinate) {
return bases.get(readCoordinate);
}
/**
public int getRefStart() {
return refStart;
}
/**
* Creates a GATKSAMRecord of the synthetic read. Will return null if the read is invalid.
*
* Invalid reads are :