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/*
* Copyright (C) 2009-2012 Institute for Computational Biomedicine,
* Weill Medical College of Cornell University
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package org.campagnelab.goby.modes;
import com.martiansoftware.jsap.JSAPException;
import com.martiansoftware.jsap.JSAPResult;
import org.campagnelab.goby.alignments.*;
import org.campagnelab.goby.reads.DualRandomAccessSequenceCache;
import org.campagnelab.goby.reads.QualityEncoding;
import org.campagnelab.goby.reads.RandomAccessSequenceInterface;
import org.campagnelab.goby.util.LogIsConfigured;
import edu.cornell.med.icb.identifier.DoubleIndexedIdentifier;
import edu.cornell.med.icb.identifier.IndexedIdentifier;
import edu.cornell.med.icb.util.VersionUtils;
import it.unimi.dsi.fastutil.ints.Int2ObjectAVLTreeMap;
import it.unimi.dsi.fastutil.ints.Int2ObjectMap;
import it.unimi.dsi.fastutil.objects.ObjectArrayList;
import it.unimi.dsi.logging.ProgressLogger;
import htsjdk.samtools.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.IOException;
import java.text.DateFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
/**
* Export a Goby alignment to the BAM format.
*
* @author Kevin Dorff
*/
public class CompactToSAMMode extends AbstractGobyMode {
/**
* Used to log debug and informational messages.
*/
private static final Logger LOG = LoggerFactory.getLogger(CompactToSAMMode.class);
private static final DateFormat GOBY_DATE_FORMAT = new SimpleDateFormat("dd:MMM:yyyy");
/**
* The mode name.
*/
private static final String MODE_NAME = "compact-to-sam";
/**
* The mode description help text.
*/
private static final String MODE_DESCRIPTION = "Exports a compact alignment to the SAM/BAM format." +
"This tool tries to export a Goby alignment comprehensively to the BAM format. Since Goby 2.0.";
/**
* For logging progress.
*/
ProgressLogger progress;
/**
* BAM/SAM output alignment filename.
*/
private String output;
/**
* Compact-alignment input basename (or one of the files of the input, such as "/path/something.entries").
*/
private String inputBasename;
/**
* The input genome in either 'compact random-access-genome' format or 'fa.gz + fa.gz.fai' format.
* The random-access-genome file can be made from the .fa.gz reference using the build-sequence-cache mode.
* If using the random-access-genome input, specify any one of the files in the random-access-genome.
* If using the 'fa.gz + fa.gz.fai' input, specify the 'fa.gz' file but make sure the '.fa.gz.fai' file
* is located in the same directory.
* Using the random-access-genome format will be considerably faster.
*/
private String inputGenome;
/**
* An "unset" value for startPosition and endPosition.
*/
private boolean hasStartOrEndPosition;
/**
* The start position for the reformat.
*/
private long startPosition;
/**
* The end position for the reformat.
*/
private long endPosition = Long.MAX_VALUE;
private QualityEncoding qualityEncoding = QualityEncoding.PHRED;
private CompactToSAMIterateAlignments alignmentIterator;
private SAMFileWriter outputSam;
private SAMFileHeader samHeader;
private SAMRecordFactory samRecordFactory;
private RandomAccessSequenceInterface genome;
private ExportableAlignmentEntryData exportData;
private Int2ObjectMap<Int2ObjectMap<ExportableAlignmentEntryData>> queryIndexToFragmentsMap;
/**
* Flag to indicate if log4j was configured.
*/
private boolean debug;
@Override
public String getModeName() {
return MODE_NAME;
}
@Override
public String getModeDescription() {
return MODE_DESCRIPTION;
}
/**
* Get the quality encoding scale used for the input fastq file.
*
* @return the quality encoding scale used for the input fastq file
*/
public QualityEncoding getQualityEncoding() {
return qualityEncoding;
}
/**
* Set the quality encoding scale to be used for the input fastq file.
* Acceptable values are "Illumina", "Sanger", and "Solexa".
*
* @param qualityEncoding the quality encoding scale to be used for the input fastq file
*/
public void setQualityEncoding(final QualityEncoding qualityEncoding) {
this.qualityEncoding = qualityEncoding;
}
public String getOutput() {
return output;
}
public void setOutput(final String output) {
this.output = output;
}
public String getInputBasename() {
return inputBasename;
}
public void setInputBasename(final String inputBasename) {
this.inputBasename = inputBasename;
}
public String getInputGenome() {
return inputGenome;
}
public void setInputGenome(final String inputGenome) {
this.inputGenome = inputGenome;
}
public long getEndPosition() {
return endPosition;
}
public void setEndPosition(final long endPosition) {
this.endPosition = endPosition;
}
public long getStartPosition() {
return startPosition;
}
public void setStartPosition(final long startPosition) {
this.startPosition = startPosition;
}
/**
* Configure.
*
* @param args command line arguments
* @return this object for chaining
* @throws java.io.IOException error parsing
* @throws com.martiansoftware.jsap.JSAPException
* error parsing
*/
@Override
public AbstractCommandLineMode configure(final String[] args) throws IOException, JSAPException {
final JSAPResult jsapResult = parseJsapArguments(args);
qualityEncoding = QualityEncoding.valueOf(jsapResult.getString("quality-encoding").toUpperCase());
// don't even dare go through the debugging code if log4j was not configured. The debug code
// is way too slow to run unintentionally in production!
inputBasename = jsapResult.getString("input-basename");
inputGenome = jsapResult.getString("genome");
output = jsapResult.getString("output");
alignmentIterator = new CompactToSAMIterateAlignments();
alignmentIterator.parseIncludeReferenceArgument(jsapResult);
genome = new DualRandomAccessSequenceCache();
try {
((DualRandomAccessSequenceCache) genome).load(inputGenome);
} catch (ClassNotFoundException e) {
throw new IOException("Could not load genome", e);
}
if (jsapResult.contains("start-position") || jsapResult.contains("end-position")) {
hasStartOrEndPosition = true;
startPosition = jsapResult.getLong("start-position", 0L);
endPosition = jsapResult.getLong("end-position", Long.MAX_VALUE);
if (startPosition < 0) {
startPosition = 0;
}
if (endPosition < 0) {
endPosition = Long.MAX_VALUE;
}
if (startPosition == 0 && endPosition == 0) {
endPosition = Long.MAX_VALUE;
}
}
if (startPosition > endPosition) {
throw new JSAPException("Start position must not be greater than the end position");
}
return this;
}
@Override
public void execute() throws IOException {
debug = LogIsConfigured.isConfigured();
queryIndexToFragmentsMap = new Int2ObjectAVLTreeMap<Int2ObjectMap<ExportableAlignmentEntryData>>();
final AlignmentReader gobyReader = new AlignmentReaderImpl(inputBasename);
gobyReader.readHeader();
final DoubleIndexedIdentifier targetIdentifiers = new DoubleIndexedIdentifier(gobyReader.getTargetIdentifiers());
gobyReader.close();
exportData = new ExportableAlignmentEntryData(genome, qualityEncoding, targetIdentifiers);
final String[] basenames = new String[1];
basenames[0] = inputBasename;
progress = new ProgressLogger(LOG);
progress.displayFreeMemory = true;
progress.start();
if (alignmentIterator == null) {
alignmentIterator = new CompactToSAMIterateAlignments();
}
final int seekTargetIndex = -1;
final String seekTargetName = "";
final int seekStartPosition = -1;
// For debugging set to a targetName, targetIndex, and startPosition
/*
final int seekTargetIndex = 10;
final String seekTargetName = "11";
final int seekStartPosition = 67675226;
*/
if (hasStartOrEndPosition) {
alignmentIterator.iterate(new FileSlice(startPosition, endPosition), basenames);
} else {
if (seekStartPosition > 0 && seekTargetIndex > 0) {
final GenomicRange range = new GenomicRange();
range.startReferenceIndex = seekTargetIndex;
range.startPosition = seekStartPosition;
range.startChromosome = seekTargetName;
range.endReferenceIndex = seekTargetIndex;
range.endPosition = seekStartPosition + 1;
range.endChromosome = seekTargetName;
alignmentIterator.iterate(range, basenames);
} else {
alignmentIterator.iterate(basenames);
}
}
if (outputSam != null) {
outputSam.close();
}
progress.stop();
}
private class CompactToSAMIterateAlignments extends IterateAlignments {
private long numWritten;
private ReadOriginInfo readOriginInfo;
private boolean hasReadGroups;
private final List<ExportableAlignmentEntryData> completeSpliceFragments;
final LinkedList<Integer> needFragmentIndexes;
final LinkedList<Integer> foundFragmentIndexes;
private CompactToSAMIterateAlignments() {
completeSpliceFragments = new ObjectArrayList<ExportableAlignmentEntryData>();
needFragmentIndexes = new LinkedList<Integer>();
foundFragmentIndexes = new LinkedList<Integer>();
}
private void initializeSam(final AlignmentReader alignmentReader) {
// Because splices cannot be written in a sorted manner, we can never consider the output to be sorted.
final boolean outputIsSorted = alignmentReader.isSorted();
// Gather the target identifiers, supply them to the SAM file
samHeader = new SAMFileHeader();
final SAMSequenceDictionary samTargetDictionary = new SAMSequenceDictionary();
final IndexedIdentifier gobyTargetIdentifiers = alignmentReader.getTargetIdentifiers();
final DoubleIndexedIdentifier gobyBackTargetIdentifiers =
new DoubleIndexedIdentifier(gobyTargetIdentifiers);
for (int i = 0; i < gobyTargetIdentifiers.size(); i++) {
final String gobyTargetName = gobyBackTargetIdentifiers.getId(i).toString();
final int gobyTargetLength = alignmentReader.getTargetLength()[i];
final SAMSequenceRecord samSequenceRecord = new SAMSequenceRecord(gobyTargetName, gobyTargetLength);
samTargetDictionary.addSequence(samSequenceRecord);
}
exportReadGroups(alignmentReader);
samHeader.setSequenceDictionary(samTargetDictionary);
final SAMProgramRecord gobyVersionProgRec = new SAMProgramRecord("Goby");
gobyVersionProgRec.setProgramVersion(VersionUtils.getImplementationVersion(GobyDriver.class));
samHeader.addProgramRecord(gobyVersionProgRec);
final SAMFileWriter samBamWriter = new SAMFileWriterFactory().
makeSAMOrBAMWriter(samHeader, outputIsSorted, new File(output));
// install a facade in front of the Sam/Bam writer to do a local sort. This is needed for spliced alignments
// whose segments are stored in a different order for Goby and BMA:
outputSam = outputIsSorted ? new BufferedSortingSamBamWriter(samBamWriter) : samBamWriter;
samRecordFactory = new DefaultSAMRecordFactory();
}
private void exportReadGroups(final AlignmentReader alignmentReader) {
readOriginInfo = alignmentReader.getReadOriginInfo();
if (readOriginInfo.size() > 0) {
hasReadGroups = true;
// Goby alignment has read origin information, export as BAM read groups:
for (final Alignments.ReadOriginInfo roi : readOriginInfo.getPbList()) {
final SAMReadGroupRecord readGroup = new SAMReadGroupRecord(roi.getOriginId());
if (roi.hasSample()) {
readGroup.setSample(roi.getSample());
}
if (roi.hasPlatform()) {
readGroup.setPlatform(roi.getPlatform());
}
if (roi.hasPlatformUnit()) {
readGroup.setPlatformUnit(roi.getPlatformUnit());
}
if (roi.hasLibrary()) {
readGroup.setLibrary(roi.getLibrary());
}
if (roi.hasRunDate()) {
final String runDate = roi.getRunDate();
try {
readGroup.setRunDate(GOBY_DATE_FORMAT.parse(runDate));
} catch (ParseException e) {
LOG.error("Unable to parse Goby date: " + runDate + " ignoring runDate read origin.");
}
}
samHeader.addReadGroup(readGroup);
}
exportData.setReadGroupInfo(readOriginInfo);
}
}
@Override
public void processAlignmentEntry(final AlignmentReader alignmentReader,
final Alignments.AlignmentEntry alignmentEntry) {
if (outputSam == null) {
initializeSam(alignmentReader);
}
exportData.buildFrom(alignmentEntry);
completeSpliceFragments.clear();
Int2ObjectMap<ExportableAlignmentEntryData> fragIndexToAlignmentsMap;
boolean splicedFragment = false;
if (alignmentEntry.hasSplicedForwardAlignmentLink() ||
alignmentEntry.hasSplicedBackwardAlignmentLink()) {
splicedFragment = true;
final int queryIndex = alignmentEntry.getQueryIndex();
fragIndexToAlignmentsMap = queryIndexToFragmentsMap.get(queryIndex);
if (fragIndexToAlignmentsMap == null) {
fragIndexToAlignmentsMap = new Int2ObjectAVLTreeMap<ExportableAlignmentEntryData>();
queryIndexToFragmentsMap.put(queryIndex, fragIndexToAlignmentsMap);
}
fragIndexToAlignmentsMap.put(exportData.getAlignmentEntry().getFragmentIndex(),
ExportableAlignmentEntryData.duplicateFrom(exportData));
findCompleteSpliceFragments(fragIndexToAlignmentsMap, queryIndexToFragmentsMap, queryIndex);
}
if (splicedFragment) {
if (!completeSpliceFragments.isEmpty()) {
outputSplicedFragments(completeSpliceFragments);
}
} else {
// This is suitable for single alignment entries or paired end
outputSingle(exportData);
}
}
/**
* Given a list of all of the fragments for a single query index, return a list of
* fragments that represent a complete splice formation. If the alignment is paired end,
* this will represent a single end of the pair, not both of the pairs.
* If none of the splices are complete, this will return null.
* If not null, this will return a NEW LIST, not the same fragIndexToAlignmentsMap list,
* additionally, the elements in the returned list will be removed from fragIndexToAlignmentsMap.
* NOTE: for performance completeSpliceFragments is used repeatedly.
*
* @param fragIndexToAlignmentsMap the list of found fragments for a desired query index.
* @param queryIndexToFragmentsMap
* @param queryIndex
*/
private void findCompleteSpliceFragments(
final Int2ObjectMap<ExportableAlignmentEntryData> fragIndexToAlignmentsMap, Int2ObjectMap<Int2ObjectMap<ExportableAlignmentEntryData>> queryIndexToFragmentsMap, int queryIndex) {
for (final Map.Entry<Integer, ExportableAlignmentEntryData> entry :
fragIndexToAlignmentsMap.entrySet()) {
// For THIS entry, see if all related forward/backward fragments exists in fragIndexToAlignmentsMap
// We need to do this for every entry in our map because this map COULD contain segments
// that span multiple alignments (such as if we are aligning ambiguity > 1 or with pairs).
needFragmentIndexes.clear();
foundFragmentIndexes.clear();
final Alignments.AlignmentEntry alignmentEntry = entry.getValue().getAlignmentEntry();
needFragmentIndexes.add(alignmentEntry.getFragmentIndex());
foundFragmentIndexes.add(alignmentEntry.getFragmentIndex());
if (alignmentEntry.hasSplicedForwardAlignmentLink()) {
walkFragments(fragIndexToAlignmentsMap,
alignmentEntry.getSplicedForwardAlignmentLink(), true);
}
if (alignmentEntry.hasSplicedBackwardAlignmentLink()) {
walkFragments(fragIndexToAlignmentsMap,
alignmentEntry.getSplicedBackwardAlignmentLink(), false);
}
// We've now walked the entire available distance, forward and backward. See if the fragment
// indexes that we need could be found.
if (foundContainsNeed(foundFragmentIndexes, needFragmentIndexes)) {
// We have a complete set of fragments
for (final int fragIndex : needFragmentIndexes) {
completeSpliceFragments.add(fragIndexToAlignmentsMap.get(fragIndex));
fragIndexToAlignmentsMap.remove(fragIndex);
}
if (needFragmentIndexes.isEmpty()) {
// since we have a complete list, we can now forget the queryIndex and its fragments:
queryIndexToFragmentsMap.remove(queryIndex);
break;
}
}
}
}
// return true if found foundFragmentIndexes is a subset of needFragmentIndexes
private boolean foundContainsNeed(LinkedList<Integer> foundFragmentIndexes, LinkedList<Integer> needFragmentIndexes) {
return foundFragmentIndexes.containsAll(needFragmentIndexes);
}
/**
* Used to walk, forward or backward, the splice fragments. Helps with determining if we have
* all the fragments for a single spliced alignment entry.
*
* @param fragIndexToAlignmentsMap the map of fragment index to alignment entry
* @param requiredRelated the related splice fragment we are walking from
* @param walkForward true if we are walking forward
*/
private void walkFragments(final Int2ObjectMap<ExportableAlignmentEntryData> fragIndexToAlignmentsMap,
final Alignments.RelatedAlignmentEntry requiredRelated, final boolean walkForward) {
final int fragmentIndex = requiredRelated.getFragmentIndex();
if (walkForward) {
// Build needFragmentIndexes, foundFragmentIndexes in the order of the aligned splices
needFragmentIndexes.addLast(fragmentIndex);
} else {
needFragmentIndexes.addFirst(fragmentIndex);
}
final ExportableAlignmentEntryData entry = fragIndexToAlignmentsMap.get(fragmentIndex);
if (entry != null) {
// The current needed entry was found. Look forward or backward for more required fragments
if (walkForward) {
foundFragmentIndexes.addLast(fragmentIndex);
} else {
foundFragmentIndexes.addFirst(fragmentIndex);
}
final Alignments.AlignmentEntry alignmentEntry = entry.getAlignmentEntry();
if (walkForward && alignmentEntry.hasSplicedForwardAlignmentLink()) {
walkFragments(fragIndexToAlignmentsMap,
alignmentEntry.getSplicedForwardAlignmentLink(), true);
}
if (!walkForward && alignmentEntry.hasSplicedBackwardAlignmentLink()) {
walkFragments(fragIndexToAlignmentsMap,
alignmentEntry.getSplicedBackwardAlignmentLink(), false);
}
}
}
private void outputSplicedFragments(final List<ExportableAlignmentEntryData> spliceFragments) {
final ExportableAlignmentEntryData exportData =
ExportableAlignmentEntryData.mergeSpliceFragments(spliceFragments);
outputSingle(exportData);
}
/**
* Output a single alignment segment. If paired end, this will output of the pair halfs.
* Spliced alignments will be written with outputMultiFragments once all the fragments of
* that alignment have bee encountered.
*
* @param toExport the alignment entry to output
*/
private void outputSingle(final ExportableAlignmentEntryData toExport) {
if (toExport.isInvalid()) {
LOG.warn(toExport.toString());
return;
}
if (debug) {
LOG.debug("Wrote qi=" + toExport.getQueryIndex() + " fragment Index=" + toExport.getAlignmentEntry().getFragmentIndex());
}
final SAMRecord samRecord = samRecordFactory.createSAMRecord(samHeader);
samRecord.setReferenceIndex(toExport.getTargetIndex());
samRecord.setFlags(toExport.getPairFlags());
samRecord.setReadName(toExport.getReadName());
samRecord.setAlignmentStart(toExport.getStartPosition());
samRecord.setMappingQuality(toExport.getMappingQuality());
samRecord.setReadString(toExport.getReadBasesOriginal());
samRecord.setBaseQualities(toExport.getReadQualities().toByteArray());
samRecord.setCigarString(toExport.getCigarString());
samRecord.setAttribute("MD", toExport.getMismatchString());
for (String bamAttribute : toExport.getBamAttributesList()) {
bamAttribute = bamAttribute.replaceAll("[\n\r]", "");
final String[] tokens = bamAttribute.split(":");
samRecord.setAttribute(tokens[0], getValue(tokens));
if (debug) {
LOG.debug(String.format("Writing %s:%s", tokens[0], getValue(tokens)));
}
}
if (toExport.hasMate()) {
samRecord.setMateReferenceIndex(toExport.getMateReferenceIndex());
samRecord.setMateAlignmentStart(toExport.getMateAlignmentStart());
samRecord.setInferredInsertSize(toExport.getInferredInsertSize());
}
if (hasReadGroups) {
samRecord.setAttribute("RG", toExport.getReadGroup());
}
try {
outputSam.addAlignment(samRecord);
} catch (RuntimeException e) {
System.out.println("entry: \n" + toExport.getAlignmentEntry().toString());
System.out.println(toExport.toString());
throw e;
}
numWritten++;
progress.lightUpdate();
}
}
private Object getValue( String[] tokens) {
if (tokens.length>3) {
String[] mergedTokens=new String[3];
mergedTokens[0]=tokens[0];
mergedTokens[1]=tokens[1];
mergedTokens[2]=tokens[2];
for (int i=3;i<tokens.length;i++) {
mergedTokens[2]+=":";
mergedTokens[2]+=tokens[i];
}
tokens=mergedTokens;
}
final String type = tokens[1];
if ("Z".equals(type)) {
return tokens[2];
}
if ("i".equals(type)) {
return Integer.parseInt(tokens[2]);
}
if ("A".equals(type)) {
return tokens[2].charAt(0);
}
LOG.warn("Attribute type %c is currently not supported, storing as string type");
return tokens[2];
}
private String getTag(final String bamAttribute) {
return bamAttribute.split(":")[0];
}
public void setGenome(RandomAccessSequenceInterface genome) {
this.genome = genome;
}
public void setGenome(String filename) throws IOException {
genome = new DualRandomAccessSequenceCache();
try {
((DualRandomAccessSequenceCache) genome).load(filename);
} catch (ClassNotFoundException e) {
throw new IOException("Could not load genome", e);
}
}
/**
* Main method.
*
* @param args command line args.
* @throws com.martiansoftware.jsap.JSAPException
* error parsing
* @throws java.io.IOException error parsing or executing.
*/
public static void main(final String[] args) throws JSAPException, IOException {
final CompactToSAMMode processor = new CompactToSAMMode();
processor.configure(args);
processor.execute();
}
}
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