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fixed hard-tabs
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@magicDGS
magicDGS committed Dec 15, 2015
1 parent b48aa0a commit 1572366
Showing 1 changed file with 67 additions and 68 deletions.
135 changes: 67 additions & 68 deletions src/java/htsjdk/samtools/util/SamLocusIterator.java
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Original file line number Diff line number Diff line change
Expand Up @@ -42,7 +42,6 @@
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import java.util.stream.Collectors;

/**
* Iterator that traverses a SAM File, accumulating information on a per-locus basis.
Expand Down Expand Up @@ -79,14 +78,14 @@ public RecordAndOffset(final SAMRecord record, final int offset) {
/**
* The unit of iteration. Holds information about the locus (the SAMSequenceRecord and 1-based position
* on the reference), plus List of ReadAndOffset objects, one for each read that overlaps the locus;
* two more List of ReadAndOffset objects includes reads that overlaps the locus with insertions/deletions
* two more List of ReadAndOffset objects includes reads that overlaps the locus with insertions/deletions
*/
public static final class LocusInfo implements Locus {
private final SAMSequenceRecord referenceSequence;
private final int position;
private final List<RecordAndOffset> recordAndOffsets = new ArrayList<RecordAndOffset>(100);
private final List<RecordAndOffset> deletedInRecord = new ArrayList<RecordAndOffset>();
private final List<RecordAndOffset> insertionInRecord = new ArrayList<RecordAndOffset>();
private final List<RecordAndOffset> deletedInRecord = new ArrayList<RecordAndOffset>();
private final List<RecordAndOffset> insertionInRecord = new ArrayList<RecordAndOffset>();

LocusInfo(final SAMSequenceRecord referenceSequence, final int position) {
this.referenceSequence = referenceSequence;
Expand All @@ -98,26 +97,26 @@ public void add(final SAMRecord read, final int position) {
recordAndOffsets.add(new RecordAndOffset(read, position));
}

/** Accumulate info for one read with a deletion */
public void addDeleted(final SAMRecord read, int previousPosition) {
deletedInRecord.add(new RecordAndOffset(read, previousPosition));
}
/** Accumulate info for one read with a deletion */
public void addDeleted(final SAMRecord read, int previousPosition) {
deletedInRecord.add(new RecordAndOffset(read, previousPosition));
}

/**
* Accumulate info for one read with an insertion.
* For this locus, the reads in the insertion are included also in recordAndOffsets
*/
public void addInsertion(final SAMRecord read, int firstPosition) {
insertionInRecord.add(new RecordAndOffset(read, firstPosition));
}
/**
* Accumulate info for one read with an insertion.
* For this locus, the reads in the insertion are included also in recordAndOffsets
*/
public void addInsertion(final SAMRecord read, int firstPosition) {
insertionInRecord.add(new RecordAndOffset(read, firstPosition));
}

public int getSequenceIndex() { return referenceSequence.getSequenceIndex(); }

/** @return 1-based reference position */
public int getPosition() { return position; }
public List<RecordAndOffset> getRecordAndPositions() { return Collections.unmodifiableList(recordAndOffsets); }
public List<RecordAndOffset> getDeletedInRecord() { return Collections.unmodifiableList(deletedInRecord); }
public List<RecordAndOffset> getInsertionInRecord() { return Collections.unmodifiableList(insertionInRecord); }
public List<RecordAndOffset> getDeletedInRecord() { return Collections.unmodifiableList(deletedInRecord); }
public List<RecordAndOffset> getInsertionInRecord() { return Collections.unmodifiableList(insertionInRecord); }
public String getSequenceName() { return referenceSequence.getSequenceName(); }
@Override public String toString() { return referenceSequence.getSequenceName() + ":" + position; }
public int getSequenceLength() {return referenceSequence.getSequenceLength();}
Expand Down Expand Up @@ -171,10 +170,10 @@ public boolean isEmpty() {
*/
private boolean emitUncoveredLoci = true;

/**
* If true, include indels in the LocusInfo
*/
private boolean includeIndels = false;
/**
* If true, include indels in the LocusInfo
*/
private boolean includeIndels = false;

// When there is a target mask, these members remember the last locus for which a LocusInfo has been
// returned, so that any uncovered locus in the target mask can be covered by a 0-coverage LocusInfo
Expand Down Expand Up @@ -353,10 +352,10 @@ public LocusInfo next() {

// Store the loci for the read in the accumulator
accumulateSamRecord(rec);
// Store the indels if requested
if(includeIndels) {
accumulateIndels(rec);
}
// Store the indels if requested
if(includeIndels) {
accumulateIndels(rec);
}
samIterator.next();
}

Expand Down Expand Up @@ -434,55 +433,55 @@ private void accumulateSamRecord(final SAMRecord rec) {
}
}

/**
* Requires that the accumulator for the record is previously fill with
/**
* Requires that the accumulator for the record is previously fill with
* {@link #accumulateSamRecord(htsjdk.samtools.SAMRecord)}.
* Include in the LocusInfo the indels; the quality threshold does not affect insertions/deletions
*/
private void accumulateIndels(final SAMRecord rec) {
// get the cigar elements
final List<CigarElement> cigar = rec.getCigar().getCigarElements();
// 0-based offset into the read of the current base
int readBase = 0;
// 0-based offset for the reference of the current base
*/
private void accumulateIndels(final SAMRecord rec) {
// get the cigar elements
final List<CigarElement> cigar = rec.getCigar().getCigarElements();
// 0-based offset into the read of the current base
int readBase = 0;
// 0-based offset for the reference of the current base
// the accumulator could have the previous position because an indel is accumulating
int refBase = 0;
// iterate over the cigar element
for (int elementIndex = 0; elementIndex < cigar.size(); elementIndex++) {
final CigarElement e = cigar.get(elementIndex);
switch (e.getOperator()) {
case H:
case P: // ignore hard clips and pads (do not consume bases)
break;
case S:
int refBase = 0;
// iterate over the cigar element
for (int elementIndex = 0; elementIndex < cigar.size(); elementIndex++) {
final CigarElement e = cigar.get(elementIndex);
switch (e.getOperator()) {
case H:
case P: // ignore hard clips and pads (do not consume bases)
break;
case S:
readBase += e.getLength();
break; // soft clip and insertions consume bases in the read
case N:
refBase += e.getLength();
break; // reference skip consume bases in the reference
case M:
case EQ:
case X:
readBase += e.getLength();
refBase += e.getLength();
break; // matches consumes both ref and read bases
case N:
refBase += e.getLength();
break; // reference skip consume bases in the reference
case M:
case EQ:
case X:
readBase += e.getLength();
refBase += e.getLength();
break; // matches consumes both ref and read bases
case I:
// insertions are included in the previous base
final int accIndex = (refBase == 0) ? 0 : refBase - 1;
accumulator.get(accIndex).addInsertion(rec, readBase);
readBase += e.getLength();
break;
case D:
// accumulate for each position that spans the deletion
for (int i = 0; i < e.getLength(); i++) {
// the offset is the one for the previous base
accumulator.get(refBase).addDeleted(rec, readBase - 1);
case D:
// accumulate for each position that spans the deletion
for (int i = 0; i < e.getLength(); i++) {
// the offset is the one for the previous base
accumulator.get(refBase).addDeleted(rec, readBase - 1);
refBase++;
}
break;
}
}
}
}
break;
}
}
}

/**
* Create the next relevant zero-coverage LocusInfo
Expand Down Expand Up @@ -615,12 +614,12 @@ public void setEmitUncoveredLoci(final boolean emitUncoveredLoci) {
this.emitUncoveredLoci = emitUncoveredLoci;
}

public boolean isIncludeIndels() {
return includeIndels;
}
public boolean isIncludeIndels() {
return includeIndels;
}

public void setIncludeIndels(final boolean includeIndels) {
this.includeIndels = includeIndels;
}
public void setIncludeIndels(final boolean includeIndels) {
this.includeIndels = includeIndels;
}
}

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