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Updated to work correctly with extended pileups. Clogged and uses some dirty tricks; pileups/extended pileups need to be redesigned someday 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3211 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2010-04-20 17:38:09 +00:00
parent 4723cad1be
commit 01e6492ba9
1 changed files with 99 additions and 35 deletions
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134
java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java
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@ -29,14 +29,9 @@ import net.sf.samtools.SAMRecord;
import net.sf.samtools.SAMReadGroupRecord; import net.sf.samtools.SAMReadGroupRecord;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup; import org.broadinstitute.sting.utils.pileup.*;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
import java.util.ArrayList; import java.util.*;
import java.util.HashMap;
import java.util.Map;
import java.util.Collection;
/** /**
* Useful class for storing different AlignmentContexts * Useful class for storing different AlignmentContexts
@ -54,45 +49,97 @@ public class StratifiedAlignmentContext {
private GenomeLoc loc; private GenomeLoc loc;
private AlignmentContext[] contexts = new AlignmentContext[StratifiedContextType.values().length]; private AlignmentContext[] contexts = new AlignmentContext[StratifiedContextType.values().length];
private boolean isExtended = false; // tells whether this alignment context is an extended event context
// todo -- why are you storing reads separately each time? There's a ReadBackedPileup object that's supposed to handle this // todo -- why are you storing reads separately each time? There's a ReadBackedPileup object that's supposed to handle this
private ArrayList<SAMRecord>[] reads = new ArrayList[StratifiedContextType.values().length]; // private ArrayList<SAMRecord>[] reads = new ArrayList[StratifiedContextType.values().length];
private ArrayList<Integer>[] offsets = new ArrayList[StratifiedContextType.values().length]; // private ArrayList<Integer>[] offsets = new ArrayList[StratifiedContextType.values().length];
private ArrayList<PileupElement>[] pileupElems = new ArrayList[StratifiedContextType.values().length];
// //
// accessors // accessors
// //
public GenomeLoc getLocation() { return loc; } public GenomeLoc getLocation() { return loc; }
public ArrayList<SAMRecord> getReads(StratifiedContextType type) { return reads[type.ordinal()]; } // public ArrayList<SAMRecord> getReads(StratifiedContextType type) { return reads[type.ordinal()]; }
public ArrayList<Integer> getOffsets(StratifiedContextType type) { return offsets[type.ordinal()]; } // public ArrayList<Integer> getOffsets(StratifiedContextType type) { return offsets[type.ordinal()]; }
public ArrayList<PileupElement> getPileupElements(StratifiedContextType type) {
return pileupElems[type.ordinal()];
}
// public ArrayList<ExtendedEventPileupElement> getExtendedPileupElements(StratifiedContextType type) {
// if ( ! isExtended ) throw new StingException("Extended read backed pileups requested from StratifiedAlignmentContext that holds simple pileups");
//
// return (ArrayList<ExtendedEventPileupElement>)(pileupElems[type.ordinal()]);
// }
public StratifiedAlignmentContext(GenomeLoc loc) { public StratifiedAlignmentContext(GenomeLoc loc) {
this(loc,false);
}
public StratifiedAlignmentContext(GenomeLoc loc, boolean isExtended) {
this.loc = loc; this.loc = loc;
this.isExtended = isExtended;
for ( int i = 0; i < StratifiedContextType.values().length; i++) { for ( int i = 0; i < StratifiedContextType.values().length; i++) {
reads[i] = new ArrayList<SAMRecord>(); if ( isExtended ) pileupElems[i] = new ArrayList<PileupElement>();
offsets[i] = new ArrayList<Integer>(); else pileupElems[i] = new ArrayList<PileupElement>();
} }
} }
public AlignmentContext getContext(StratifiedContextType type) { public AlignmentContext getContext(StratifiedContextType type) {
int index = type.ordinal(); int index = type.ordinal();
if ( contexts[index] == null ) if ( contexts[index] == null ) {
contexts[index] = new AlignmentContext(loc, new ReadBackedPileup(loc, getReads(type), getOffsets(type))); if ( isExtended ) {
contexts[index] = new AlignmentContext(loc , new ReadBackedExtendedEventPileup(loc, (ArrayList<ExtendedEventPileupElement>)((ArrayList<? extends PileupElement>)getPileupElements(type))));
} else {
contexts[index] = new AlignmentContext(loc, new ReadBackedPileup(loc, getPileupElements(type)));
}
}
return contexts[index]; return contexts[index];
} }
public void add(SAMRecord read, int offset) { public void add(SAMRecord read, int offset) {
if ( isExtended ) throw new StingException("Can not add read/offset without event type specified to the context holding extended events");
if ( read.getReadNegativeStrandFlag() ) { if ( read.getReadNegativeStrandFlag() ) {
reads[StratifiedContextType.REVERSE.ordinal()].add(read); pileupElems[StratifiedContextType.REVERSE.ordinal()].add(new PileupElement(read,offset));
offsets[StratifiedContextType.REVERSE.ordinal()].add(offset);
} else { } else {
reads[StratifiedContextType.FORWARD.ordinal()].add(read); pileupElems[StratifiedContextType.FORWARD.ordinal()].add(new PileupElement(read,offset));
offsets[StratifiedContextType.FORWARD.ordinal()].add(offset);
} }
reads[StratifiedContextType.COMPLETE.ordinal()].add(read); pileupElems[StratifiedContextType.COMPLETE.ordinal()].add(new PileupElement(read,offset));
offsets[StratifiedContextType.COMPLETE.ordinal()].add(offset);
} }
public void add(PileupElement p) {
// if ( isExtended ) throw new StingException("Can not add simple pileup element to the context holding extended events");
SAMRecord read = p.getRead();
if ( read.getReadNegativeStrandFlag() ) {
pileupElems[StratifiedContextType.REVERSE.ordinal()].add(p);
} else {
pileupElems[StratifiedContextType.FORWARD.ordinal()].add(p);
}
pileupElems[StratifiedContextType.COMPLETE.ordinal()].add(p);
}
public void add(SAMRecord read, int offset, int length, byte [] bases) {
if ( ! isExtended ) throw new StingException("Can not add read/offset with event type specified to the context holding simple events");
if ( read.getReadNegativeStrandFlag() ) {
pileupElems[StratifiedContextType.REVERSE.ordinal()].add(new ExtendedEventPileupElement(read,offset,length,bases));
} else {
pileupElems[StratifiedContextType.FORWARD.ordinal()].add(new ExtendedEventPileupElement(read,offset,length,bases));
}
pileupElems[StratifiedContextType.COMPLETE.ordinal()].add(new ExtendedEventPileupElement(read,offset,length,bases));
}
// public void add(ExtendedEventPileupElement p) {
// if ( ! isExtended ) throw new StingException("Can not add extended pileup element to the context holding simple events");
// SAMRecord read = p.getRead();
// if ( read.getReadNegativeStrandFlag() ) {
// pileupElems[StratifiedContextType.REVERSE.ordinal()].add(p);
// } else {
// pileupElems[StratifiedContextType.FORWARD.ordinal()].add(p);
// }
// pileupElems[StratifiedContextType.COMPLETE.ordinal()].add(p);
// }
/** /**
* Splits the given AlignmentContext into a StratifiedAlignmentContext per sample. * Splits the given AlignmentContext into a StratifiedAlignmentContext per sample.
* *
@ -154,12 +201,17 @@ public class StratifiedAlignmentContext {
GenomeLoc loc = pileup.getLocation(); GenomeLoc loc = pileup.getLocation();
for (PileupElement p : pileup ) for (PileupElement p : pileup )
addToContext(contexts, p, loc, assumedSingleSample, collapseToThisSample); addToContext(contexts, p, loc, assumedSingleSample, collapseToThisSample,true);
return contexts; return contexts;
} }
private static void addToContext(HashMap<String, StratifiedAlignmentContext> contexts, PileupElement p, GenomeLoc loc, String assumedSingleSample, String collapseToThisSample) { private static void addToContext(HashMap<String, StratifiedAlignmentContext> contexts, PileupElement p, GenomeLoc loc, String assumedSingleSample, String collapseToThisSample) {
addToContext(contexts, p, loc, assumedSingleSample, collapseToThisSample, false);
}
private static void addToContext(HashMap<String, StratifiedAlignmentContext> contexts, PileupElement p, GenomeLoc loc, String assumedSingleSample, String collapseToThisSample, boolean isExtended) {
// get the read // get the read
SAMRecord read = p.getRead(); SAMRecord read = p.getRead();
@ -181,13 +233,13 @@ public class StratifiedAlignmentContext {
// create a new context object if this is the first time we're seeing a read for this sample // create a new context object if this is the first time we're seeing a read for this sample
StratifiedAlignmentContext myContext = contexts.get(sample); StratifiedAlignmentContext myContext = contexts.get(sample);
if ( myContext == null ) { if ( myContext == null ) {
myContext = new StratifiedAlignmentContext(loc); myContext = new StratifiedAlignmentContext(loc,isExtended);
contexts.put(sample, myContext); contexts.put(sample, myContext);
} }
// add the read to this sample's context // add the read to this sample's context
// note that bad bases are added to the context (for DoC calculations later) // note that bad bases are added to the context (for DoC calculations later)
myContext.add(read, p.getOffset()); myContext.add(p);
} }
/** /**
@ -218,25 +270,37 @@ public class StratifiedAlignmentContext {
contexts.put(group,myContext); contexts.put(group,myContext);
} }
myContext.add(read,p.getOffset()); myContext.add(p);
} }
return contexts; return contexts;
} }
public static AlignmentContext joinContexts(Collection<StratifiedAlignmentContext> contexts, StratifiedContextType type) { public static AlignmentContext joinContexts(Collection<StratifiedAlignmentContext> contexts, StratifiedContextType type) {
ArrayList<SAMRecord> reads = new ArrayList<SAMRecord>(); ArrayList<PileupElement> pe = new ArrayList();
ArrayList<Integer> offsets = new ArrayList<Integer>();
GenomeLoc loc = null; if ( contexts.size() == 0 )
for ( StratifiedAlignmentContext context : contexts ) { throw new StingException("BUG: joinContexts requires at least one context to join");
loc = context.getLocation();
reads.addAll(context.getReads(type));
offsets.addAll(context.getOffsets(type)); Iterator<StratifiedAlignmentContext> it = contexts.iterator();
StratifiedAlignmentContext context = it.next();
boolean isExtended = context.isExtended;
GenomeLoc loc = context.getLocation();
pe.addAll(context.getPileupElements(type));
while ( it.hasNext()) {
context = it.next();
if ( ! loc.equals( context.getLocation() ) )
throw new StingException("Illegal attempt to join contexts from different genomic locations");
if ( context.isExtended != isExtended )
throw new StingException("Illegal attempt to join simple and extended contexts");
pe.addAll(context.getPileupElements(type));
} }
if ( loc == null ) // dirty trick below. generics do not allow to cast pe (ArrayList<PileupElement>) directly to ArrayList<ExtendedEventPileupElement>,
throw new StingException("BUG: joinContexts requires at least one context to join"); // so we first cast to "? extends" wildcard, then to what we actually need.
return new AlignmentContext(loc, new ReadBackedPileup(loc, reads, offsets)); if ( isExtended ) return new AlignmentContext(loc, new ReadBackedExtendedEventPileup(loc, (ArrayList< ExtendedEventPileupElement>)((ArrayList<? extends PileupElement>)pe)) );
else return new AlignmentContext(loc, new ReadBackedPileup(loc,pe));
} }
} }