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package org.broadinstitute.gatk.tools.walkers.indels;
import htsjdk.samtools.SamPairUtil;
import htsjdk.samtools.SAMFileWriter;
import htsjdk.samtools.SAMRecord;
import htsjdk.samtools.SAMRecordComparator;
import htsjdk.samtools.SAMRecordCoordinateComparator;
import org.apache.log4j.Logger;
import org.broadinstitute.gatk.utils.GenomeLoc;
import org.broadinstitute.gatk.utils.GenomeLocParser;
import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.sam.GATKSAMRecord;
import java.util.*;
/*
* Copyright (c) 2009 The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
/**
* A locally resorting, mate fixing sam file writer that supports an idiom where reads are only moved around if
* the ISIZE of the pair is < X and reads are not allowed to move any more than Y bp from their original positions.
*
* To understand this data structure, let's begin by asking -- when are we certain we know the position of read R added
* to the writer and its mate M given that R has been added to the writer (but M may not be), their ISIZE in R, at the
* moment that a read K is added to the writer, under the constraints X and Y? Complex I know. First, because
* reads cannot move more than Y bp in either direction, we know that R originated at most R.pos + Y bp from its
* current position. Also, we know that K is at most K.pos + Y bp from it's original position. If R is maximally
* shifted to the right, and K shifted to the left, then they could at most move 2Y together. So if the distance
* between R and K > 2Y, we know that there are no reads left in the original stream that could be moved before R.
*
* Now, we also need to be certain if we have a mate pair M, that won't emit R before we can incorporate any move of
* M into the mate pair info R. There are two cases to consider here:
*
* If ISIZE > X, we know that we won't move M when we see it, so we can safely emit R knowing that
* M is fixed in place.
*
* If ISIZE <= X, M might be moved, and it we have to wait until we see M in the stream to know it's position.
* So R must be buffered until either M arrives, or we see a read K that's more than 2Y units past the original position
* of M.
*
* So the worst-case memory consumption here is proportional to the number of reads
* occurring between R and M + 2 Y, and so is proportional to the depth of the data and X and Y.
*
* This leads to the following simple algorithm:
*
* addAlignment(newRead):
* addReadToListOfReads(newRead)
* update mate pair of newRead if present in list of reads
*
* for ( read in list of reads [in order of increasing read.pos] ):
* if read.pos < newRead.pos - 2Y && (read.isize >= X || read.matePos < newRead.pos - 2 * Y):
* emit read and remove from list of reads
* else:
* break
*
* @author depristo, ebanks
* @version 0.2
*/
public class ConstrainedMateFixingManager {
protected static final Logger logger = Logger.getLogger(ConstrainedMateFixingManager.class);
private static final boolean DEBUG = false;
/** How often do we check whether we want to emit reads? */
protected final static int EMIT_FREQUENCY = 1000;
/**
* How much could a single read move in position from its original position?
*/
final int MAX_POS_MOVE_ALLOWED;
/**
* How many reads should we store in memory before flushing the queue?
*/
final int MAX_RECORDS_IN_MEMORY;
/** how we order our SAM records */
private final SAMRecordComparator comparer = new SAMRecordCoordinateComparator();
/** The place where we ultimately write out our records */
final SAMFileWriter writer;
/**
* what is the maximum isize of a pair of reads that can move? Reads with isize > this value
* are assumes to not be allowed to move in the incoming read stream.
*/
final int maxInsertSizeForMovingReadPairs;
final int initialCapacity = 5000;
final GenomeLocParser genomeLocParser;
private GenomeLoc lastLocFlushed = null;
int counter = 0;
/** read.name -> records */
HashMap<String, SAMRecordHashObject> forMateMatching = new HashMap<String, SAMRecordHashObject>();
PriorityQueue<SAMRecord> waitingReads = new PriorityQueue<SAMRecord>(initialCapacity, comparer);
private SAMRecord remove(PriorityQueue<SAMRecord> queue) {
SAMRecord first = queue.poll();
if (first == null)
throw new UserException("Error caching SAM record -- priority queue is empty, and yet there was an attempt to poll it -- which is usually caused by malformed SAM/BAM files in which multiple identical copies of a read are present.");
return first;
}
private static class SAMRecordHashObject {
public SAMRecord record;
public boolean wasModified;
public SAMRecordHashObject(SAMRecord record, boolean wasModified) {
this.record = record;
this.wasModified = wasModified;
}
}
//private SimpleTimer timer = new SimpleTimer("ConstrainedWriter");
//private long PROGRESS_PRINT_FREQUENCY = 10 * 1000; // in milliseconds
//private long lastProgressPrintTime = -1; // When was the last time we printed progress log?
/**
*
* @param writer actual writer
* @param genomeLocParser the GenomeLocParser object
* @param maxInsertSizeForMovingReadPairs max insert size allowed for moving pairs
* @param maxMoveAllowed max positional move allowed for any read
* @param maxRecordsInMemory max records to keep in memory
*/
public ConstrainedMateFixingManager(final SAMFileWriter writer,
final GenomeLocParser genomeLocParser,
final int maxInsertSizeForMovingReadPairs,
final int maxMoveAllowed,
final int maxRecordsInMemory) {
this.writer = writer;
this.genomeLocParser = genomeLocParser;
this.maxInsertSizeForMovingReadPairs = maxInsertSizeForMovingReadPairs;
this.MAX_POS_MOVE_ALLOWED = maxMoveAllowed;
this.MAX_RECORDS_IN_MEMORY = maxRecordsInMemory;
//timer.start();
//lastProgressPrintTime = timer.currentTime();
}
public int getNReadsInQueue() { return waitingReads.size(); }
/**
* For testing purposes only
*
* @return the list of reads currently in the queue
*/
protected List<SAMRecord> getReadsInQueueForTesting() {
return new ArrayList<SAMRecord>(waitingReads);
}
public boolean canMoveReads(GenomeLoc earliestPosition) {
if ( DEBUG ) logger.info("Refusing to realign? " + earliestPosition + " vs. " + lastLocFlushed);
return lastLocFlushed == null ||
lastLocFlushed.compareContigs(earliestPosition) != 0 ||
lastLocFlushed.distance(earliestPosition) > maxInsertSizeForMovingReadPairs;
}
private boolean noReadCanMoveBefore(int pos, SAMRecord addedRead) {
return pos + 2 * MAX_POS_MOVE_ALLOWED < addedRead.getAlignmentStart();
}
public void addRead(SAMRecord newRead, boolean readWasModified) {
addRead(newRead, readWasModified, true);
}
public void addReads(List<GATKSAMRecord> newReads, Set<GATKSAMRecord> modifiedReads) {
for ( GATKSAMRecord newRead : newReads )
addRead(newRead, modifiedReads.contains(newRead), false);
}
protected void addRead(SAMRecord newRead, boolean readWasModified, boolean canFlush) {
if ( DEBUG ) logger.info("New read pos " + newRead.getAlignmentStart() + " OP = " + newRead.getAttribute("OP") + " " + readWasModified);
//final long curTime = timer.currentTime();
//if ( curTime - lastProgressPrintTime > PROGRESS_PRINT_FREQUENCY ) {
// lastProgressPrintTime = curTime;
// System.out.println("WaitingReads.size = " + waitingReads.size() + ", forMateMatching.size = " + forMateMatching.size());
//}
// if the new read is on a different contig or we have too many reads, then we need to flush the queue and clear the map
boolean tooManyReads = getNReadsInQueue() >= MAX_RECORDS_IN_MEMORY;
if ( (canFlush && tooManyReads) || (getNReadsInQueue() > 0 && !waitingReads.peek().getReferenceIndex().equals(newRead.getReferenceIndex())) ) {
if ( DEBUG ) logger.warn("Flushing queue on " + (tooManyReads ? "too many reads" : ("move to new contig: " + newRead.getReferenceName() + " from " + waitingReads.peek().getReferenceName())) + " at " + newRead.getAlignmentStart());
while ( getNReadsInQueue() > 1 ) {
// emit to disk
writeRead(remove(waitingReads));
}
SAMRecord lastRead = remove(waitingReads);
lastLocFlushed = (lastRead.getReferenceIndex() == -1) ? null : genomeLocParser.createGenomeLoc(lastRead);
writeRead(lastRead);
if ( !tooManyReads )
forMateMatching.clear();
else
purgeUnmodifiedMates();
}
// fix mates, as needed
// Since setMateInfo can move reads, we potentially need to remove the mate, and requeue
// it to ensure proper sorting
if ( newRead.getReadPairedFlag() && !newRead.getNotPrimaryAlignmentFlag() ) {
SAMRecordHashObject mate = forMateMatching.get(newRead.getReadName());
if ( mate != null ) {
// 1. Frustratingly, Picard's setMateInfo() method unaligns (by setting the reference contig
// to '*') read pairs when both of their flags have the unmapped bit set. This is problematic
// when trying to emit reads in coordinate order because all of a sudden we have reads in the
// middle of the bam file that now belong at the end - and any mapped reads that get emitted
// after them trigger an exception in the writer. For our purposes, because we shouldn't be
// moving read pairs when they are both unmapped anyways, we'll just not run fix mates on them.
// 2. Furthermore, when reads get mapped to the junction of two chromosomes (e.g. MT since it
// is actually circular DNA), their unmapped bit is set, but they are given legitimate coordinates.
// The Picard code will come in and move the read all the way back to its mate (which can be
// arbitrarily far away). However, we do still want to move legitimately unmapped reads whose
// mates are mapped, so the compromise will be that if the mate is still in the queue then we'll
// move the read and otherwise we won't.
boolean doNotFixMates = newRead.getReadUnmappedFlag() && (mate.record.getReadUnmappedFlag() || !waitingReads.contains(mate.record));
if ( !doNotFixMates ) {
boolean reQueueMate = mate.record.getReadUnmappedFlag() && ! newRead.getReadUnmappedFlag();
if ( reQueueMate ) {
// the mate was unmapped, but newRead was mapped, so the mate may have been moved
// to be next-to newRead, so needs to be reinserted into the waitingReads queue
// note -- this must be called before the setMateInfo call below
if ( ! waitingReads.remove(mate.record) )
// we must have hit a region with too much depth and flushed the queue
reQueueMate = false;
}
// we've already seen our mate -- set the mate info and remove it from the map
// Via Nils Homer:
// There will be two SamPairUtil.setMateInfo functions. The default will not update the mate
// cigar tag; in fact, it will remove it if it is present. An alternative SamPairUtil.setMateInfo
// function takes a boolean as an argument ("addMateCigar") and will add/update the mate cigar if
// set to true. This is the one you want to use.
SamPairUtil.setMateInfo(mate.record, newRead, null, true);
if ( reQueueMate ) waitingReads.add(mate.record);
}
forMateMatching.remove(newRead.getReadName());
} else if ( pairedReadIsMovable(newRead) ) {
forMateMatching.put(newRead.getReadName(), new SAMRecordHashObject(newRead, readWasModified));
}
}
waitingReads.add(newRead);
if ( ++counter % EMIT_FREQUENCY == 0 ) {
while ( ! waitingReads.isEmpty() ) { // there's something in the queue
SAMRecord read = waitingReads.peek();
if ( noReadCanMoveBefore(read.getAlignmentStart(), newRead) &&
(!pairedReadIsMovable(read) // we won't try to move such a read
|| noReadCanMoveBefore(read.getMateAlignmentStart(), newRead ) ) ) { // we're already past where the mate started
// remove reads from the map that we have emitted -- useful for case where the mate never showed up
if ( !read.getNotPrimaryAlignmentFlag() )
forMateMatching.remove(read.getReadName());
if ( DEBUG )
logger.warn(String.format("EMIT! At %d: read %s at %d with isize %d, mate start %d, op = %s",
newRead.getAlignmentStart(), read.getReadName(), read.getAlignmentStart(),
read.getInferredInsertSize(), read.getMateAlignmentStart(), read.getAttribute("OP")));
// emit to disk
writeRead(remove(waitingReads));
} else {
if ( DEBUG )
logger.warn(String.format("At %d: read %s at %d with isize %d couldn't be emited, mate start %d",
newRead.getAlignmentStart(), read.getReadName(), read.getAlignmentStart(), read.getInferredInsertSize(), read.getMateAlignmentStart()));
break;
}
}
if ( DEBUG ) logger.warn(String.format("At %d: Done with emit cycle", newRead.getAlignmentStart()));
}
}
private void writeRead(SAMRecord read) {
try {
if ( writer != null )
writer.addAlignment(read);
} catch (IllegalArgumentException e) {
throw new UserException("If the maximum allowable reads in memory is too small, it may cause reads to be written out of order when trying to write the BAM; please see the --maxReadsInMemory argument for details. " + e.getMessage(), e);
}
}
/**
* @param read the read
* @return true if the read shouldn't be moved given the constraints of this SAMFileWriter
*/
public boolean iSizeTooBigToMove(SAMRecord read) {
return iSizeTooBigToMove(read, maxInsertSizeForMovingReadPairs); // we won't try to move such a read
}
public static boolean iSizeTooBigToMove(SAMRecord read, int maxInsertSizeForMovingReadPairs) {
return ( read.getReadPairedFlag() && ! read.getMateUnmappedFlag() && !read.getReferenceName().equals(read.getMateReferenceName()) ) // maps to different chromosomes
|| Math.abs(read.getInferredInsertSize()) > maxInsertSizeForMovingReadPairs; // we won't try to move such a read
}
private void purgeUnmodifiedMates() {
HashMap<String, SAMRecordHashObject> forMateMatchingCleaned = new HashMap<String, SAMRecordHashObject>();
for ( Map.Entry<String, SAMRecordHashObject> entry : forMateMatching.entrySet() ) {
if ( entry.getValue().wasModified )
forMateMatchingCleaned.put(entry.getKey(), entry.getValue());
}
forMateMatching.clear(); // explicitly clear the memory
forMateMatching = forMateMatchingCleaned;
}
private boolean pairedReadIsMovable(SAMRecord read) {
return read.getReadPairedFlag() // we're a paired read
&& (!read.getReadUnmappedFlag() || !read.getMateUnmappedFlag()) // at least one read is mapped
&& !iSizeTooBigToMove(read); // insert size isn't too big
}
public void close() {
// write out all of the remaining reads
while ( ! waitingReads.isEmpty() ) { // there's something in the queue
writeRead(remove(waitingReads));
}
}
}