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Fix for ROD in TraversalEngine 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@18 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-03-02 02:46:34 +00:00
parent b19e4b502b
commit 63f8d82e36
5 changed files with 45 additions and 19 deletions
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2
java/src/edu/mit/broad/sting/atk/PrepareROD.java
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@ -48,7 +48,6 @@ public class PrepareROD extends CommandLineProgram {
final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE_ARG);
List<SAMSequenceRecord> refContigs = refFile.getSequenceDictionary();
HashMap<String, Integer> refContigOrdering = new HashMap<String, Integer>();
ReferenceOrderedDatum.setContigOrdering(refContigOrdering);
int i = 0;
for ( SAMSequenceRecord contig : refContigs ) {
@ -56,6 +55,7 @@ public class PrepareROD extends CommandLineProgram {
refContigOrdering.put(contig.getSequenceName(), i);
i++;
}
ReferenceOrderedDatum.setContigOrdering(refContigOrdering);
Class rodClass = Types.get(ROD_TYPE.toLowerCase());

2
java/src/edu/mit/broad/sting/atk/TraversalEngine.java
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@ -11,6 +11,7 @@ import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
import edu.mit.broad.sting.utils.ReferenceIterator;
import edu.mit.broad.sting.utils.ReferenceOrderedData;
import edu.mit.broad.sting.utils.ReferenceOrderedDatum;
import edu.mit.broad.sting.utils.Utils;
import java.io.*;
import java.util.List;
@ -89,6 +90,7 @@ public class TraversalEngine {
if ( refFileName!= null ) {
this.refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(refFileName);
this.refIter = new ReferenceIterator(this.refFile);
Utils.setupRefContigOrdering(this.refFile);
}
}

5
java/src/edu/mit/broad/sting/utils/ReferenceOrderedData.java
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@ -146,7 +146,7 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
while ( hasNext() ) {
ROD current = next();
//System.out.printf(" -> Seeking to %s %d AT %s %d%n", contigName, pos, current.getContig(), current.getStart());
int strCmp = contigName.compareTo( prev.getContig() );
int strCmp = ReferenceOrderedDatum.compareContigs( contigName, prev.getContig() );// contigName.compareTo( prev.getContig() );
if ( strCmp == 0 ) {
// The contigs are equal
if ( current.getStart() > pos ) {
@ -161,8 +161,9 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
}
}
else if ( strCmp < 0 ) {
if ( DEBUG ) System.out.printf(" -> Jumping to contig %s%n", contigName);
if ( DEBUG ) System.out.printf(" -> Jumped to contig %s%n", contigName);
// We've gone past the desired contig, break
it.pushback(current);
break;
}
}

35
java/src/edu/mit/broad/sting/utils/ReferenceOrderedDatum.java
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@ -31,40 +31,43 @@ public abstract class ReferenceOrderedDatum implements Comparable {
public abstract long getStart();
public abstract long getStop();
public int compareTo( Object x ) {
if ( this == x ) return 0;
ReferenceOrderedDatum that = (ReferenceOrderedDatum)x;
public static int compareContigs( final String thisContig, final String thatContig ) {
if ( refContigOrdering != null ) {
if ( ! refContigOrdering.containsKey(this.getContig()) ) {
if ( ! refContigOrdering.containsKey(that.getContig()) ) {
if ( ! refContigOrdering.containsKey(thisContig) ) {
if ( ! refContigOrdering.containsKey(thatContig) ) {
// Use regular sorted order
int cmpContig = getContig().compareTo(that.getContig());
if ( cmpContig != 0 )return cmpContig;
return thisContig.compareTo(thatContig);
}
else {
// this is always bigger if that is in the key set
return 1;
}
}
else if ( ! refContigOrdering.containsKey(that.getContig()) )
else if ( ! refContigOrdering.containsKey(thatContig) )
return -1;
else {
assert refContigOrdering.containsKey(this.getContig()) : this;
assert refContigOrdering.containsKey(that.getContig()) : that;
assert refContigOrdering.containsKey(thisContig);// : this;
assert refContigOrdering.containsKey(thatContig);// : that;
final int thisO = refContigOrdering.get(this.getContig());
final int thatO = refContigOrdering.get(that.getContig());
final int thisO = refContigOrdering.get(thisContig);
final int thatO = refContigOrdering.get(thatContig);
if ( thisO < thatO ) return -1;
if ( thisO > thatO ) return 1;
return 0;
}
}
else {
int cmpContig = getContig().compareTo(that.getContig());
if ( cmpContig != 0 )return cmpContig;
return thisContig.compareTo(thatContig);
}
}
public int compareTo( Object x ) {
if ( this == x ) return 0;
ReferenceOrderedDatum that = (ReferenceOrderedDatum)x;
final int cmpContig = compareContigs( this.getContig(), that.getContig() );
if ( cmpContig != 0 ) return cmpContig;
if ( this.getStart() < that.getStart() ) return -1;
if ( this.getStart() > that.getStart() ) return 1;
if ( this.getStop() < that.getStop() ) return -1;

20
java/src/edu/mit/broad/sting/utils/Utils.java
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@ -1,6 +1,10 @@
package edu.mit.broad.sting.utils;
import edu.mit.broad.sam.SAMRecord;
import edu.mit.broad.sam.SAMSequenceRecord;
import edu.mit.broad.picard.reference.ReferenceSequenceFileFactory;
import edu.mit.broad.picard.reference.ReferenceSequence;
import edu.mit.broad.picard.reference.ReferenceSequenceFile;
import java.util.*;
@ -63,4 +67,20 @@ public class Utils {
}
return ret.toString();
}
public static void setupRefContigOrdering(final ReferenceSequenceFile refFile) {
List<SAMSequenceRecord> refContigs = refFile.getSequenceDictionary();
HashMap<String, Integer> refContigOrdering = new HashMap<String, Integer>();
int i = 0;
System.out.printf("Prepared reference sequence contig dictionary%n order ->");
for ( SAMSequenceRecord contig : refContigs ) {
System.out.printf(" %s", contig.getSequenceName());
refContigOrdering.put(contig.getSequenceName(), i);
i++;
}
System.out.printf("%n Total elements -> %d%n", refContigOrdering.size());
ReferenceOrderedDatum.setContigOrdering(refContigOrdering);
}
}