225 lines
8.3 KiB
Java
Executable File
225 lines
8.3 KiB
Java
Executable File
/*
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* Copyright (c) 2009 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.contexts;
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import net.sf.samtools.SAMRecord;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
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import org.broadinstitute.sting.gatk.iterators.LocusOverflowTracker;
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import java.util.*;
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/**
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* Useful class for forwarding on locusContext data from this iterator
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*
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* Created by IntelliJ IDEA.
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* User: mdepristo
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* Date: Feb 22, 2009
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* Time: 3:01:34 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class AlignmentContext {
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protected GenomeLoc loc = null;
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protected ReadBackedPileup basePileup = null;
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protected ReadBackedExtendedEventPileup extendedPileup = null;
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private LocusOverflowTracker tracker;
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/**
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* The number of bases we've skipped over in the reference since the last map invocation.
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* Only filled in by RodTraversals right now. By default, nothing is being skipped, so skippedBases == 0.
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*/
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private long skippedBases = 0;
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/**
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* Default constructor for AlignmentContext object
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* since private objects are already set to null we
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* don't need to do anything
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*/
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public AlignmentContext() { /* private objects already set to null */ }
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/**
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* Create a new AlignmentContext object
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*
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* @param loc
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* @param reads
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* @param offsets
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*/
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@Deprecated
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public AlignmentContext(GenomeLoc loc, List<SAMRecord> reads, List<Integer> offsets) {
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this(loc, reads, offsets, 0);
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}
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@Deprecated
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public AlignmentContext(GenomeLoc loc, List<SAMRecord> reads, List<Integer> offsets, long skippedBases ) {
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if ( loc == null ) throw new StingException("BUG: GenomeLoc in Alignment context is null");
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if ( skippedBases < 0 ) throw new StingException("BUG: skippedBases is -1 in Alignment context");
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this.loc = loc;
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this.basePileup = new ReadBackedPileup(loc, reads, offsets);
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this.skippedBases = skippedBases;
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}
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public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup) {
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this(loc, basePileup, 0);
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}
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public AlignmentContext(GenomeLoc loc, ReadBackedExtendedEventPileup extendedPileup) {
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this(loc, extendedPileup, 0);
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}
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public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup, long skippedBases ) {
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if ( loc == null ) throw new StingException("BUG: GenomeLoc in Alignment context is null");
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if ( basePileup == null ) throw new StingException("BUG: ReadBackedPileup in Alignment context is null");
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if ( skippedBases < 0 ) throw new StingException("BUG: skippedBases is -1 in Alignment context");
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this.loc = loc;
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this.basePileup = basePileup;
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this.skippedBases = skippedBases;
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}
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public AlignmentContext(GenomeLoc loc, ReadBackedExtendedEventPileup extendedPileup, long skippedBases ) {
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if ( loc == null ) throw new StingException("BUG: GenomeLoc in Alignment context is null");
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if ( extendedPileup == null ) throw new StingException("BUG: ReadBackedExtendedEventPileup in Alignment context is null");
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if ( skippedBases < 0 ) throw new StingException("BUG: skippedBases is -1 in Alignment context");
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this.loc = loc;
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this.extendedPileup = extendedPileup;
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this.skippedBases = skippedBases;
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}
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/** Returns base pileup over the current genomic location. Deprectated. Use getBasePileup() to make your intentions
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* clear.
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* @return
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*/
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@Deprecated
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public ReadBackedPileup getPileup() { return basePileup; }
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/** Returns base pileup over the current genomic location. May return null if this context keeps only
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* extended event (indel) pileup.
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* @return
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*/
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public ReadBackedPileup getBasePileup() { return basePileup; }
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/** Returns extended event (indel) pileup over the current genomic location. May return null if this context keeps
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* only base pileup.
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* @return
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*/
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public ReadBackedExtendedEventPileup getExtendedEventPileup() { return extendedPileup; }
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/** Returns true if this alignment context keeps base pileup over the current genomic location.
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*
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* @return
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*/
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public boolean hasBasePileup() { return basePileup != null; }
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/** Returns true if this alignment context keeps extended event (indel) pileup over the current genomic location.
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*
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* @return
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*/
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public boolean hasExtendedEventPileup() { return extendedPileup != null; }
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/**
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* get all of the reads within this context
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*
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* @return
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*/
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@Deprecated
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//todo: unsafe and tailored for current usage only; both pileups can be null or worse, bot can be not null in theory
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public List<SAMRecord> getReads() { return ( basePileup == null ? extendedPileup.getReads() : basePileup.getReads() ); }
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/**
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* Are there any reads associated with this locus?
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*
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* @return
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*/
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public boolean hasReads() {
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return ( (basePileup != null && basePileup.size() > 0) || (extendedPileup != null && extendedPileup.size() > 0) ) ;
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}
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/**
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* How many reads cover this locus?
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* @return
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*/
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public int size() {
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if ( basePileup == null && extendedPileup == null ) return 0;
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//todo: both pileups can be non-nulls in theory (but not in current usage), what if sizes differ?
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return extendedPileup == null ? basePileup.size() : extendedPileup.size();
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}
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/**
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* get a list of the equivalent positions within in the reads at Pos
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*
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* @return
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*/
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@Deprecated
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public List<Integer> getOffsets() {
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//todo: both pileups can be non-nulls in theory (but not in current usage), what offsets should we return?
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return extendedPileup == null ? basePileup.getOffsets() : extendedPileup.getOffsets();
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}
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public String getContig() { return getLocation().getContig(); }
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public long getPosition() { return getLocation().getStart(); }
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public GenomeLoc getLocation() { return loc; }
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public void downsampleToCoverage(int coverage) {
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if ( basePileup != null ) {
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basePileup = basePileup.getDownsampledPileup(coverage);
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}
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if ( extendedPileup != null ) {
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extendedPileup = extendedPileup.getDownsampledPileup(coverage);
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}
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}
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/**
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* Returns the number of bases we've skipped over in the reference since the last map invocation.
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* Only filled in by RodTraversals right now. A value of 0 indicates that no bases were skipped.
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*
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* @return the number of skipped bases
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*/
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public long getSkippedBases() {
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return skippedBases;
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}
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/**
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* a method for injecting the current locus overflow tracker into the alignment context.
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* @param state
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*/
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public void setLocusOverflowTracker(LocusOverflowTracker state) {
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this.tracker = state;
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}
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/**
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* have we exceeded the maximum pileup at the current locus?
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* @return true if we have, false otherwise
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*/
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public boolean hasExceededMaxPileup() {
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if (this.tracker == null) return false;
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return this.tracker.inDroppedRegion(getLocation());
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}
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}
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