Fixed genome loc to be immutable, the only way to now change it's values is through the GenomeLocParser.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1132 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/LocusContext.java

@@ -1,15 +1,10 @@
 package org.broadinstitute.sting.gatk;
 
-import net.sf.samtools.SAMRecord;
-
-import java.util.List;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.TreeSet;
-import java.util.Random;
-
-import org.broadinstitute.sting.utils.GenomeLoc;
 import net.sf.picard.reference.ReferenceSequence;
+import net.sf.samtools.SAMRecord;
+import org.broadinstitute.sting.utils.GenomeLoc;
+
+import java.util.*;
 
 /**
  * Useful class for forwarding on locusContext data from this iterator
@@ -81,7 +76,9 @@ public class LocusContext {
     public String getContig() { return getLocation().getContig(); }
     public long getPosition() { return getLocation().getStart(); }
     public GenomeLoc getLocation() { return loc; }
-
+    public void setLocation(GenomeLoc loc) {
+        this.loc = loc.clone();
+    }
     /**
      * Returns the entire reference sequence contig associated with these reads
      *

java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java

@@ -180,7 +180,7 @@ public class SAMDataSource implements SimpleDataSource {
                 iter = iteratorPool.iterator(new MappedStreamSegment(lastReadPos));
                 return InitialReadIterator(shard.getSize(), iter);
             } else {
-                lastReadPos.setStop(-1);
+                lastReadPos = GenomeLocParser.setStop(lastReadPos,-1);
                 iter = fastMappedReadSeek(shard.getSize(), StingSAMIteratorAdapter.adapt(reads, iteratorPool.iterator(new MappedStreamSegment(lastReadPos))));
             }
 
@@ -267,7 +267,7 @@ public class SAMDataSource implements SimpleDataSource {
                 } else {
                     readsTaken = readCount;
                     readsSeenAtLastPos = 0;
-                    lastReadPos.setStop(-1);
+                    lastReadPos = GenomeLocParser.setStop(lastReadPos,-1);
                     CloseableIterator<SAMRecord> ret = iteratorPool.iterator(new MappedStreamSegment(lastReadPos));
                     return new BoundedReadIterator(StingSAMIteratorAdapter.adapt(reads, ret), readCount);
                 }
@@ -285,7 +285,7 @@ public class SAMDataSource implements SimpleDataSource {
             if (stopPos < lastReadPos.getStart()) {
                 lastReadPos = GenomeLocParser.createGenomeLoc(lastReadPos.getContigIndex() + 1, stopPos, stopPos);
             } else {
-                lastReadPos.setStart(rec.getAlignmentStart());
+                lastReadPos = GenomeLocParser.setStart(lastReadPos,rec.getAlignmentStart());
             }
         }
         // in case we're run out of reads, get out

java/src/org/broadinstitute/sting/gatk/iterators/GenomeLocusIterator.java

@@ -34,7 +34,7 @@ public class GenomeLocusIterator implements LocusIterator {
     /**
      * Creates an iterator that can traverse over the entire
      * reference specified in the given ShardDataProvider.
-     * @param provider Data provider to use as a backing source.
+     * @param completeLocus Data provider to use as a backing source.
      *                 Provider must have a reference (hasReference() == true).
      */
     public GenomeLocusIterator( GenomeLoc completeLocus ) {
@@ -58,7 +58,7 @@ public class GenomeLocusIterator implements LocusIterator {
         if( !hasNext() )
             throw new NoSuchElementException("No elements remaining in bounded reference region.");
         GenomeLoc toReturn = (GenomeLoc)currentLocus.clone();
-        currentLocus.incPos();
+        currentLocus = GenomeLocParser.incPos(currentLocus);
         return toReturn;
     }
 

java/src/org/broadinstitute/sting/gatk/traversals/TraverseByLocusWindows.java

@@ -1,21 +1,31 @@
 package org.broadinstitute.sting.gatk.traversals;
 
+import net.sf.picard.sam.SamFileHeaderMerger;
+import net.sf.samtools.SAMFileHeader;
+import net.sf.samtools.SAMFileReader;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.util.CloseableIterator;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.Reads;
+import org.broadinstitute.sting.gatk.iterators.MergingSamRecordIterator2;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
+import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.LocusWindowWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.*;
+import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.gatk.refdata.*;
+import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.gatk.iterators.MergingSamRecordIterator2;
+import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.fasta.*;
+import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 
-import java.util.*;
+import java.io.File;
-import java.io.*;
+import java.io.FileNotFoundException;
-
+import java.util.ArrayList;
-import net.sf.samtools.SAMRecord;
+import java.util.Collections;
-import net.sf.samtools.SAMFileReader;
+import java.util.Iterator;
-import net.sf.samtools.SAMFileHeader;
+import java.util.List;
-import net.sf.samtools.util.CloseableIterator;
-import net.sf.picard.sam.SamFileHeaderMerger;
 
 /**
  * Created by IntelliJ IDEA.
@@ -136,7 +146,7 @@ public class TraverseByLocusWindows extends TraversalEngine {
         String refSuffix = "";
         if ( window.getLocation().getStop() > contigLength ) {
             refSuffix = Utils.dupString('x', (int)window.getLocation().getStop() - contigLength);
-            window.getLocation().setStop(contigLength);
+            window.setLocation(GenomeLocParser.setStop(window.getLocation(),contigLength));
         }
 
         StringBuffer refBases = new StringBuffer(new String(sequenceFile.getSubsequenceAt(window.getContig(),window.getLocation().getStart(),window.getLocation().getStop()).getBases()));

java/src/org/broadinstitute/sting/playground/gatk/walkers/FastaReferenceWalker.java

@@ -5,6 +5,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Pair;
 
 // create a fasta sequence file from a reference and intervals
@@ -34,7 +35,7 @@ public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, Character>,
         }
         // otherwise, merge them
         else {
-            sum.first.setStop(value.first.getStop());
+            sum.first = GenomeLocParser.setStop(sum.first,value.first.getStop());
             sum.second = new String(sum.second + value.second);
         }
 		return sum;

java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/CoverageGapIntervalWalker.java

@@ -58,7 +58,7 @@ public class CoverageGapIntervalWalker extends LocusWalker<Pair<GenomeLoc, Integ
     public GenomeLoc reduce(Pair<GenomeLoc, Integer> value, GenomeLoc sum) {
         if ( value.second > 1000 ) {
             if ( sum != null )
-                sum.setStop(value.first.getStop());
+                sum = GenomeLocParser.setStop(sum,value.first.getStop());
             else
                 sum = value.first;
         } else if ( sum != null ) {

java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IndelGenotyperWalker.java

@@ -1,29 +1,22 @@
 package org.broadinstitute.sting.playground.gatk.walkers.indels;
 
-import java.io.IOException;
+import net.sf.samtools.*;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Set;
-
-import net.sf.samtools.Cigar;
-import net.sf.samtools.CigarElement;
-import net.sf.samtools.CigarOperator;
-import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMFileReader;
-import net.sf.samtools.SAMReadGroupRecord;
-import net.sf.samtools.SAMRecord;
-
 import org.broadinstitute.sting.gatk.refdata.RODIterator;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.rodRefSeq;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.playground.utils.CircularArray;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
 
 public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
 	@Argument(fullName="bed", shortName="bed", doc="BED output file name", required=true)
@@ -189,7 +182,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
 			currentContigIndex = read.getReferenceIndex();
 			currentPosition = read.getAlignmentStart();
 			refName = new String(read.getReferenceName());
-			location.setContig(refName);
+			location = GenomeLocParser.setContig(location,refName);
 			
 			coverage.clear(); // reset coverage window; this will also set reference position to 0
 			if ( call_somatic) normal_coverage.clear();
@@ -315,7 +308,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
 				continue; // too dirty
 			}
 			
-			location.setStart(pos); location.setStop(pos); // retrieve annotation data
+			location = GenomeLocParser.setStart(location,pos); location = GenomeLocParser.setStop(location,pos); // retrieve annotation data
 			rodRefSeq annotation = (refseqIterator == null ? null : refseqIterator.seekForward(location));
 
 			int total_variant_count = 0;
@@ -412,7 +405,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
 				"\tTUMOR TOO DIRTY\t"+total_mismatches_tumor);
 				continue; // too dirty
 			}
-			location.setStart(pos); location.setStop(pos); // retrieve annotation data
+			location = GenomeLocParser.setStart(location,pos); location = GenomeLocParser.setStop(location,pos); // retrieve annotation data
 			rodRefSeq annotation = (refseqIterator == null ? null : refseqIterator.seekForward(location));
 			
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalMergerWalker.java

@@ -84,7 +84,7 @@ public class IntervalMergerWalker extends ReadWalker<Integer,Integer> {
         // at this point, we're in the first interval.
         // now we can merge any other intervals which we overlap
         while ( intervals.size() > 0 && loc.overlapsP(intervals.getFirst()) )
-            firstInterval.setStop(intervals.removeFirst().getStop());
+            firstInterval = GenomeLocParser.setStop(firstInterval,intervals.removeFirst().getStop());
 
         return 1;
     }

java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/MismatchIntervalWalker.java

@@ -93,17 +93,17 @@ public class MismatchIntervalWalker extends LocusWalker<Pair<GenomeLoc, Boolean>
             // if there is no interval to the left, then this is the first one
             if ( sum.second == null ) {
                 sum.second = value.first;
-                sum.second.setStart(sum.second.getStart() - windowSize + firstMismatch + 1);
+                sum.second = GenomeLocParser.setStart(sum.second, sum.second.getStart() - windowSize + firstMismatch + 1);
             }
             // if the intervals don't overlap, print out the leftmost one and start a new one
             else if ( value.first.getStop() - sum.second.getStop() > windowSize ) {
                 out.println(sum.second);
                 sum.second = value.first;
-                sum.second.setStart(sum.second.getStart() - windowSize + firstMismatch + 1);
+                sum.second = GenomeLocParser.setStart(sum.second,sum.second.getStart() - windowSize + firstMismatch + 1);
             }
             // otherwise, merge them
             else {
-                sum.second.setStop(value.first.getStop());
+                sum.second = GenomeLocParser.setStop(sum.second, value.first.getStop());
             }
         }
 

java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/SNPClusterWalker.java

@@ -54,7 +54,7 @@ public class SNPClusterWalker extends RefWalker<GenomeLoc, GenomeLoc> {
 
         // if the last SNP location was within a window, merge them
         if ( value.getStart() - sum.getStop() <= windowSize ) {
-            sum.setStop(value.getStart());            
+            sum = GenomeLocParser.setStop(sum,value.getStart());            
             return sum;
         }
 

java/src/org/broadinstitute/sting/utils/GenomeLoc.java

@@ -23,12 +23,11 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
      * the basic components of a genome loc, its contig index,
      * start and stop position, and (optionally) the contig name
      */
-    private int contigIndex;
+    protected final int contigIndex;
-    private long start;
+    protected final long start;
-    private long stop;
+    protected final long stop;
-    private String contigName;
+    protected final String contigName;
-    static int MAX_CONTIG;
+    
-
     // --------------------------------------------------------------------------------------------------------------
     //
     // constructors
@@ -146,28 +145,6 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
     public final boolean throughEndOfContigP() { return this.stop == Integer.MAX_VALUE; }
     public final boolean atBeginningOfContigP() { return this.start == 1; }
 
-    /** Sets contig name. UNSAFE since it 1) does NOT update contig index; 2) does not validate the name
-     * 
-     * @param contig
-     */
-    public void setContig(String contig) {
-        this.contigName = contig;
-    }
-
-    /** Sets contig index. UNSAFE since it 1) does NOT update contig name; 2) does not validate the index
-     * 
-     * @param contig
-     */
-    public void setContigIndex(int contig) {
-        this.contigIndex = contig;
-    }
-
-    public void setStart(long start) {
-        this.start = start;
-    }
-    public void setStop(long stop) {
-        this.stop = stop;
-    }
 
     public final boolean isSingleBP() { return stop == start; }
 
@@ -230,19 +207,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
         return ( comparison == 1 || ( comparison == 0 && this.getStart() > that.getStop() ));
     }
 
-    public final void incPos() {
+    
-        incPos(1);
-    }
-    public final void incPos(long by) {
-        this.start += by;
-        this.stop += by;
-    }
-
-    public final GenomeLoc nextLoc() {
-        GenomeLoc n = new GenomeLoc(this);
-        n.incPos();
-        return n;
-    }
 
     /**
      * Check to see whether two genomeLocs are equal.

java/src/org/broadinstitute/sting/utils/GenomeLocParser.java

@@ -124,7 +124,6 @@ public class GenomeLocParser {
                 logger.debug(String.format(" %s (%d bp)", contig.getSequenceName(), contig.getSequenceLength()));
             }
         }
-        GenomeLoc.MAX_CONTIG = contigInfo.getSequences().size();
         return true;
     }
 
@@ -221,7 +220,7 @@ public class GenomeLocParser {
             logger.debug("Locations are:" + Utils.join(", ", locs));
             return locs;
         } catch (Exception e) { // TODO: fix this so that it passes the message from the exception, and doesn't print it out
-            throw new StingException(String.format("Invalid locations string: %s, format is loc1;loc2; where each locN can be 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'", str),e);
+            throw new StingException(String.format("Invalid locations string: %s, format is loc1;loc2; where each locN can be 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'", str), e);
         }
     }
 
@@ -446,14 +445,10 @@ public class GenomeLocParser {
      * @return the genome loc if it's valid, otherwise we throw an exception
      */
     private static GenomeLoc verifyGenomeLoc(GenomeLoc toReturn) {
-        // conditions to fail on - we currently use a start of zero to indicate infinite read count, so don't check for that
-        //if ((toReturn.getStop() < toReturn.getStart())) {
-        //    throw new StingException("Parameters to GenomeLocParser are incorrect: the start position is after the stop (Start = " + toReturn.getStart() + " stop = " + toReturn.getStop() + ")");
-        //}
         if (toReturn.getStart() < 0) {
             throw new StingException("Parameters to GenomeLocParser are incorrect: the start position is less than 0");
         }
-        if (toReturn.getStop() < 0) {
+        if ((toReturn.getStop() != -1) && (toReturn.getStop() < 0)) {
             throw new StingException("Parameters to GenomeLocParser are incorrect: the stop position is less than 0");
         }
         if (toReturn.getContigIndex() < 0) {
@@ -483,8 +478,102 @@ public class GenomeLocParser {
     }
 
     /**
-     * check to make sure that we've setup the contig information
+     * create a new genome loc, given an old location and a new contig
+     *
+     * @param loc    the old location
+     * @param contig the new contig to set
+     *
+     * @return a new genome loc with an updated contig name and index
      */
+    public static GenomeLoc setContig(GenomeLoc loc, String contig) {
+        checkSetup();
+        if (!GenomeLocParser.contigInfo.getSequences().contains(contig)) {
+            throw new StingException("Contig name ( " + contig + " ) not in the set sequence dictionary.");
+        }
+        return verifyGenomeLoc(new GenomeLoc(contig, GenomeLocParser.contigInfo.getSequences().indexOf(contig), loc.start, loc.getStop()));
+    }
+
+/** Sets contig index. UNSAFE since it 1) does NOT update contig name; 2) does not validate the index
+     *
+     * @param contig
+     */
+    public static GenomeLoc setContigIndex(GenomeLoc loc, int contig) {
+        checkSetup();
+        if ((contig >= GenomeLocParser.contigInfo.getSequences().size()) || (contig < 0)) {
+            throw new StingException("Contig index ( " + contig + " ) is not in the sequence dictionary set.");
+        }
+        return verifyGenomeLoc(new GenomeLoc(GenomeLocParser.contigInfo.getSequence(contig).getSequenceName(), contig, loc.start, loc.getStop()));
+    }
+
+
+
+    /**
+     * create a new genome loc from an existing loc, with a new start position
+     *
+     * @param loc   the old location
+     * @param start a new start position
+     *
+     * @return the newly created genome loc
+     */
+    public static GenomeLoc setStart(GenomeLoc loc, long start) {
+        checkSetup();
+        if (loc.getContigIndex() < 0 || loc.getContigIndex() >= contigInfo.getSequences().size()) {
+            throw new StingException("Genome loc passed in to setStart has a contig index outside the range of our current sequence dictionary");
+        }
+        if (start > GenomeLocParser.contigInfo.getSequences().get(loc.getContigIndex()).getSequenceLength()) {
+            throw new StingException("start value of " + start + " is greater than the contig length, and is not -1.");
+        }
+        return verifyGenomeLoc(new GenomeLoc(loc.getContig(), loc.getContigIndex(), start, loc.getStop()));
+    }
+
+    /**
+     * create a new genome loc from an existing loc, with a new stop position
+     *
+     * @param loc  the old location
+     * @param stop a new stop position
+     *
+     * @return
+     */
+    public static GenomeLoc setStop(GenomeLoc loc, long stop) {
+        checkSetup();
+        if (loc.getContigIndex() < 0 || loc.getContigIndex() >= contigInfo.getSequences().size()) {
+            throw new StingException("Genome loc passed in to setStart has a contig index outside the range of our current sequence dictionary");
+        }
+        if ((stop != -1) && (stop > GenomeLocParser.contigInfo.getSequences().get(loc.getContigIndex()).getSequenceLength())) {
+            throw new StingException("stop value of " + stop + " is greater than the contig length, and is not -1.");
+        }
+        return verifyGenomeLoc(new GenomeLoc(loc.getContig(), loc.getContigIndex(), loc.start, stop));
+    }
+
+    /**
+     * return a new genome loc, with an incremented position
+     * @param loc the old location
+     * @return a new genome loc
+     */
+    public static GenomeLoc incPos(GenomeLoc loc) {
+        return incPos(loc, 1);
+    }
+
+    /**
+     * return a new genome loc, with an incremented position
+     * @param loc the old location
+     * @param by how much to move the start and stop by
+     * @return a new genome loc
+     */
+    public static GenomeLoc incPos(GenomeLoc loc, long by) {
+        return verifyGenomeLoc(new GenomeLoc(loc.getContig(), loc.getContigIndex(), loc.start + by, loc.stop + by));
+    }
+
+    /**
+     * create a new genome loc with an incremented position
+     * @param loc the location
+     * @return a new genome loc
+     */
+    public static GenomeLoc nextLoc(GenomeLoc loc) {
+        return incPos(loc);
+    }
+
+    /** check to make sure that we've setup the contig information */
     private static void checkSetup() {
         if (contigInfo == null) {
             throw new StingException("The GenomeLocParser hasn't been setup with a contig sequence yet");

java/src/org/broadinstitute/sting/utils/RefHanger.java

@@ -1,11 +1,10 @@
 package org.broadinstitute.sting.utils;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.apache.log4j.Logger;
 
-import java.util.List;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.List;
 
 /**
  * Hanging data off the reference sequence
@@ -271,12 +270,12 @@ public class RefHanger<T> {
         else {
             //assert pos.compareTo(getRightLoc()) == 1 : pos + " " + getRightLoc() + " => " + pos.compareTo(getRightLoc());
 
-            GenomeLoc nextRight = getRightLoc().nextLoc();
+            GenomeLoc nextRight = GenomeLocParser.nextLoc(getRightLoc());
             while (pos.compareTo(nextRight) == 1) {
                 //printState();
                 //System.out.printf("    *** Extending %s, heading for %s%n", nextRight, pos);
                 ensurePos(nextRight);
-                nextRight = nextRight.nextLoc();
+                nextRight = GenomeLocParser.nextLoc(nextRight);
             }
 
             ensurePos(pos);

java/test/org/broadinstitute/sting/utils/RefHangerTest.java

@@ -83,10 +83,10 @@ public class RefHangerTest extends BaseTest {
         l4 = Arrays.asList(7, 8);
         l5 = Arrays.asList(9, 10);
         p1 = GenomeLocParser.createGenomeLoc(0, 1, 1);
-        p2 = new GenomeLoc(p1).nextLoc();
+        p2 = GenomeLocParser.nextLoc(p1);
-        p3 = new GenomeLoc(p2).nextLoc();
+        p3 = GenomeLocParser.nextLoc(p2);
-        p4 = new GenomeLoc(p3).nextLoc();
+        p4 = GenomeLocParser.nextLoc(p3);
-        p5 = new GenomeLoc(p4).nextLoc();
+        p5 = GenomeLocParser.nextLoc(p4);
 
         filledHanger.addDataList(Arrays.asList(p1, p2, p3, p4, p5),
                                  Arrays.asList(l1, l2, l3, l4, l5));