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Sam2CramRecordFactory.java
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Sam2CramRecordFactory.java
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/*******************************************************************************
* Copyright 2013 EMBL-EBI
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
******************************************************************************/
package htsjdk.samtools.cram.build;
import htsjdk.samtools.CigarElement;
import htsjdk.samtools.CigarOperator;
import htsjdk.samtools.SAMFileHeader;
import htsjdk.samtools.SAMReadGroupRecord;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecord.SAMTagAndValue;
import htsjdk.samtools.SAMTag;
import htsjdk.samtools.cram.encoding.read_features.BaseQualityScore;
import htsjdk.samtools.cram.encoding.read_features.Deletion;
import htsjdk.samtools.cram.encoding.read_features.HardClip;
import htsjdk.samtools.cram.encoding.read_features.InsertBase;
import htsjdk.samtools.cram.encoding.read_features.Padding;
import htsjdk.samtools.cram.encoding.read_features.ReadFeature;
import htsjdk.samtools.cram.encoding.read_features.RefSkip;
import htsjdk.samtools.cram.encoding.read_features.SoftClip;
import htsjdk.samtools.cram.encoding.read_features.Substitution;
import htsjdk.samtools.cram.mask.RefMaskUtils;
import htsjdk.samtools.cram.structure.CramCompressionRecord;
import htsjdk.samtools.cram.structure.ReadTag;
import htsjdk.samtools.util.Log;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.TreeSet;
public class Sam2CramRecordFactory {
public static final String UNKNOWN_READ_GROUP_ID = "UNKNOWN";
public static final String UNKNOWN_READ_GROUP_SAMPLE = "UNKNOWN";
public final static byte QS_asciiOffset = 33;
public final static byte unsetQualityScore = 32;
public final static byte ignorePositionsWithQualityScore = -1;
private byte[] refBases;
private byte[] refSNPs;
private RefMaskUtils.RefMask refPile;
private static Log log = Log.getInstance(Sam2CramRecordFactory.class);
private Map<String, Integer> readGroupMap = new HashMap<String, Integer>();
private long landedRefMaskScores = 0;
private long landedPiledScores = 0;
private long landedTotalScores = 0;
public boolean captureAllTags = false;
public boolean preserveReadNames = false;
public Set<String> captureTags = new TreeSet<String>();
public Set<String> ignoreTags = new TreeSet<String>();
{
ignoreTags.add(SAMTag.NM.name());
ignoreTags.add(SAMTag.MD.name());
ignoreTags.add(SAMTag.RG.name());
}
public boolean losslessQS = false;
private List<ReadTag> readTagList = new ArrayList<ReadTag>();
private long baseCount = 0;
private long featureCount = 0;
public Sam2CramRecordFactory(int samSequenceIndex, byte[] refBases,
SAMFileHeader samFileHeader) {
this.refBases = refBases;
List<SAMReadGroupRecord> readGroups = samFileHeader.getReadGroups();
for (int i = 0; i < readGroups.size(); i++) {
SAMReadGroupRecord readGroupRecord = readGroups.get(i);
readGroupMap.put(readGroupRecord.getId(), i);
}
}
public CramCompressionRecord createCramRecord(SAMRecord record) {
CramCompressionRecord cramRecord = new CramCompressionRecord();
if (record.getReadPairedFlag()) {
cramRecord.mateAlignmentStart = record.getMateAlignmentStart();
cramRecord.setMateUmapped(record.getMateUnmappedFlag());
cramRecord
.setMateNegativeStrand(record.getMateNegativeStrandFlag());
cramRecord.mateSequenceID = record.getMateReferenceIndex();
} else
cramRecord.mateSequenceID = -1;
cramRecord.sequenceId = record.getReferenceIndex();
cramRecord.readName = record.getReadName();
cramRecord.alignmentStart = record.getAlignmentStart();
cramRecord.setMultiFragment(record.getReadPairedFlag());
cramRecord.setProperPair(record.getReadPairedFlag()
&& record.getProperPairFlag());
cramRecord.setSegmentUnmapped(record.getReadUnmappedFlag());
cramRecord.setNegativeStrand(record.getReadNegativeStrandFlag());
cramRecord.setFirstSegment(record.getReadPairedFlag()
&& record.getFirstOfPairFlag());
cramRecord.setLastSegment(record.getReadPairedFlag()
&& record.getSecondOfPairFlag());
cramRecord.setSecondaryAlignment(record.getNotPrimaryAlignmentFlag());
cramRecord.setVendorFiltered(record
.getReadFailsVendorQualityCheckFlag());
cramRecord.setDuplicate(record.getDuplicateReadFlag());
cramRecord.readLength = record.getReadLength();
cramRecord.mappingQuality = record.getMappingQuality();
cramRecord.setDuplicate(record.getDuplicateReadFlag());
cramRecord.templateSize = record.getInferredInsertSize();
SAMReadGroupRecord readGroup = record.getReadGroup();
if (readGroup != null)
cramRecord.readGroupID = readGroupMap.get(readGroup.getId());
else
cramRecord.readGroupID = -1;
if (!record.getReadPairedFlag())
cramRecord.setLastSegment(false);
else {
if (record.getFirstOfPairFlag())
cramRecord.setLastSegment(false);
else if (record.getSecondOfPairFlag())
cramRecord.setLastSegment(true);
else
cramRecord.setLastSegment(true);
}
if (!record.getReadUnmappedFlag()
&& record.getAlignmentStart() != SAMRecord.NO_ALIGNMENT_START) {
List<ReadFeature> features = checkedCreateVariations(cramRecord,
record);
cramRecord.readFeatures = features;
} else
cramRecord.readFeatures = Collections.emptyList();
cramRecord.readBases = record.getReadBases();
cramRecord.qualityScores = record.getBaseQualities();
landedTotalScores += cramRecord.readLength;
readTagList.clear();
if (captureAllTags) {
List<SAMTagAndValue> attributes = record.getAttributes();
for (SAMTagAndValue tv : attributes) {
if (ignoreTags.contains(tv.tag))
continue;
readTagList.add(ReadTag.deriveTypeFromValue(tv.tag, tv.value));
}
} else {
if (!captureTags.isEmpty()) {
List<SAMTagAndValue> attributes = record.getAttributes();
cramRecord.tags = new ReadTag[attributes.size()];
for (SAMTagAndValue tv : attributes) {
if (captureTags.contains(tv.tag)) {
readTagList.add(ReadTag.deriveTypeFromValue(tv.tag,
tv.value));
}
}
}
}
cramRecord.tags = (ReadTag[]) readTagList
.toArray(new ReadTag[readTagList.size()]);
cramRecord.setVendorFiltered(record
.getReadFailsVendorQualityCheckFlag());
if (preserveReadNames)
cramRecord.readName = record.getReadName();
return cramRecord;
}
/**
* A wrapper method to provide better diagnostics for
* ArrayIndexOutOfBoundsException.
*
* @param cramRecord
* @param samRecord
* @return
*/
private List<ReadFeature> checkedCreateVariations(
CramCompressionRecord cramRecord, SAMRecord samRecord) {
try {
return createVariations(cramRecord, samRecord);
} catch (ArrayIndexOutOfBoundsException e) {
log.error("Reference bases array length=" + refBases.length);
log.error("Offensive CRAM record: " + cramRecord.toString());
log.error("Offensive SAM record: " + samRecord.getSAMString());
throw e;
}
}
private List<ReadFeature> createVariations(
CramCompressionRecord cramRecord, SAMRecord samRecord) {
List<ReadFeature> features = new LinkedList<ReadFeature>();
int zeroBasedPositionInRead = 0;
int alignmentStartOffset = 0;
int cigarElementLength = 0;
List<CigarElement> cigarElements = samRecord.getCigar()
.getCigarElements();
byte[] bases = samRecord.getReadBases();
byte[] qualityScore = samRecord.getBaseQualities();
for (CigarElement cigarElement : cigarElements) {
cigarElementLength = cigarElement.getLength();
CigarOperator operator = cigarElement.getOperator();
switch (operator) {
case D:
features.add(new Deletion(zeroBasedPositionInRead + 1,
cigarElementLength));
break;
case N:
features.add(new RefSkip(zeroBasedPositionInRead + 1,
cigarElementLength));
break;
case P:
features.add(new Padding(zeroBasedPositionInRead + 1,
cigarElementLength));
break;
case H:
features.add(new HardClip(zeroBasedPositionInRead + 1,
cigarElementLength));
break;
case S:
addSoftClip(features, zeroBasedPositionInRead,
cigarElementLength, bases, qualityScore);
break;
case I:
addInsertion(features, zeroBasedPositionInRead,
cigarElementLength, bases, qualityScore);
break;
case M:
case X:
case EQ:
addSubstitutionsAndMaskedBases(cramRecord, features,
zeroBasedPositionInRead, alignmentStartOffset,
cigarElementLength, bases, qualityScore);
break;
default:
throw new IllegalArgumentException(
"Unsupported cigar operator: "
+ cigarElement.getOperator());
}
if (cigarElement.getOperator().consumesReadBases())
zeroBasedPositionInRead += cigarElementLength;
if (cigarElement.getOperator().consumesReferenceBases())
alignmentStartOffset += cigarElementLength;
}
this.baseCount += bases.length;
this.featureCount += features.size();
return features;
}
private void addSoftClip(List<ReadFeature> features,
int zeroBasedPositionInRead, int cigarElementLength, byte[] bases,
byte[] scores) {
byte[] insertedBases = Arrays.copyOfRange(bases,
zeroBasedPositionInRead, zeroBasedPositionInRead
+ cigarElementLength);
SoftClip v = new SoftClip(zeroBasedPositionInRead + 1, insertedBases);
features.add(v);
}
private void addInsertion(List<ReadFeature> features,
int zeroBasedPositionInRead, int cigarElementLength, byte[] bases,
byte[] scores) {
byte[] insertedBases = Arrays.copyOfRange(bases,
zeroBasedPositionInRead, zeroBasedPositionInRead
+ cigarElementLength);
for (int i = 0; i < insertedBases.length; i++) {
// single base insertion:
InsertBase ib = new InsertBase();
ib.setPosition(zeroBasedPositionInRead + 1 + i);
ib.setBase(insertedBases[i]);
features.add(ib);
}
}
private void addSubstitutionsAndMaskedBases(
CramCompressionRecord cramRecord, List<ReadFeature> features,
int fromPosInRead, int alignmentStartOffset, int nofReadBases,
byte[] bases, byte[] qualityScore) {
int oneBasedPositionInRead;
boolean noQS = (qualityScore.length == 0);
int i = 0;
boolean qualityAdded = false;
byte refBase;
for (i = 0; i < nofReadBases; i++) {
oneBasedPositionInRead = i + fromPosInRead + 1;
int refCoord = (int) (cramRecord.alignmentStart + i + alignmentStartOffset) - 1;
qualityAdded = false;
if (refCoord >= refBases.length)
refBase = 'N';
else
refBase = refBases[refCoord];
refBase = Utils.normalizeBase(refBase);
if (bases[i + fromPosInRead] != refBase) {
Substitution sv = new Substitution();
sv.setPosition(oneBasedPositionInRead);
sv.setBase(bases[i + fromPosInRead]);
sv.setRefernceBase(refBase);
sv.setBaseChange(null);
features.add(sv);
if (losslessQS || noQS)
continue;
}
if (noQS)
continue;
if (!qualityAdded && refSNPs != null) {
byte snpOrNot = refSNPs[refCoord];
if (snpOrNot != 0) {
byte score = (byte) (QS_asciiOffset + qualityScore[i
+ fromPosInRead]);
features.add(new BaseQualityScore(oneBasedPositionInRead,
score));
qualityAdded = true;
landedRefMaskScores++;
}
}
if (!qualityAdded && refPile != null) {
if (refPile.shouldStore(refCoord, refBase)) {
byte score = (byte) (QS_asciiOffset + qualityScore[i
+ fromPosInRead]);
features.add(new BaseQualityScore(oneBasedPositionInRead,
score));
qualityAdded = true;
landedPiledScores++;
}
}
if (qualityAdded)
landedTotalScores++;
}
}
public long getLandedRefMaskScores() {
return landedRefMaskScores;
}
public long getLandedPiledScores() {
return landedPiledScores;
}
public long getLandedTotalScores() {
return landedTotalScores;
}
public byte[] getRefBases() {
return refBases;
}
public void setRefBases(byte[] refBases) {
this.refBases = refBases;
}
public byte[] getRefSNPs() {
return refSNPs;
}
public void setRefSNPs(byte[] refSNPs) {
this.refSNPs = refSNPs;
}
public RefMaskUtils.RefMask getRefPile() {
return refPile;
}
public Map<String, Integer> getReadGroupMap() {
return readGroupMap;
}
public void setRefPile(RefMaskUtils.RefMask refPile) {
this.refPile = refPile;
}
public long getBaseCount() {
return baseCount;
}
public long getFeatureCount() {
return featureCount;
}
}