Aaron: 1, GenomeLoc: 0. I changed our GenomeLoc class, seperating the creation of a genome loc (with the reference setup) to a parser class. GenomeLoc now just represents the actual genomic postion. The constructors are now package-protected (to enforce using the parser), but we may want to expose some constructors in the future.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1069 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -101,7 +101,7 @@ public class GenomeAnalysisEngine {
         // Prepare the sort ordering w.r.t. the sequence dictionary
         if (argCollection.referenceFile != null) {
             final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(argCollection.referenceFile);
-            GenomeLoc.setupRefContigOrdering(refFile);
+            GenomeLocParser.setupRefContigOrdering(refFile);
         }
 
         // Determine the validation stringency.  Default to ValidationStringency.STRICT.
@@ -145,7 +145,7 @@ public class GenomeAnalysisEngine {
         // Prepare the sort ordering w.r.t. the sequence dictionary
         if (argCollection.referenceFile != null) {
             final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(argCollection.referenceFile);
-            GenomeLoc.setupRefContigOrdering(refFile);
+            GenomeLocParser.setupRefContigOrdering(refFile);
         }
 
         // Determine the validation stringency.  Default to ValidationStringency.STRICT.
@@ -222,10 +222,10 @@ public class GenomeAnalysisEngine {
         if ( intervalsString != null) {
             if (new File(intervalsString).exists()) {
                 if (! quiet) logger.info("Intervals argument specifies a file.  Loading intervals from file.");
-                locs = GenomeLoc.IntervalFileToList(intervalsString);
+                locs = GenomeLocParser.intervalFileToList(intervalsString);
             } else {
                 if (! quiet) logger.info("Intervals argument does not specify a file.  Trying to parse it as a simple string.");
-                locs = GenomeLoc.parseGenomeLocs(intervalsString);
+                locs = GenomeLocParser.parseGenomeLocs(intervalsString);
             }
         }
         return locs;

java/src/org/broadinstitute/sting/gatk/datasources/shards/LocusShardStrategy.java

@@ -5,6 +5,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.Iterator;
 /**
@@ -63,7 +64,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
     LocusShardStrategy( SAMSequenceDictionary dic ) {
         this.dic = dic;
         limitingFactor = -1;
-        mLoc = new GenomeLoc(0, 0, 0);
+        mLoc = GenomeLocParser.createGenomeLoc(0, 0, 0);
         if (dic.getSequences().size() > 0) {
             nextContig = true;
         }
@@ -98,7 +99,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
             throw new IllegalArgumentException("Interval files must contain at least one interval");
         }
         GenomeLoc loc = intervals.iterator().next();
-        mLoc = new GenomeLoc(loc.getContig(), loc.getStart() - 1, loc.getStart() - 1);
+        mLoc = GenomeLocParser.createGenomeLoc(loc.getContig(), loc.getStart() - 1, loc.getStart() - 1);
         if (dic.getSequences().size() > 0) {
             nextContig = true;
         }
@@ -174,7 +175,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
             intervals.removeRegion(loc);
             return new IntervalShard(loc);
         } else {
-            GenomeLoc subLoc = new GenomeLoc(loc.getContigIndex(), loc.getStart(), loc.getStart() + proposedSize - 1);
+            GenomeLoc subLoc = GenomeLocParser.createGenomeLoc(loc.getContigIndex(), loc.getStart(), loc.getStart() + proposedSize - 1);
             intervals.removeRegion(subLoc);
             return new IntervalShard(subLoc);
         }
@@ -193,7 +194,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
         // can we fit it into the current seq size?
         if (nextStart + proposedSize - 1 < length) {
             lastGenomeLocSize = proposedSize;
-            mLoc = new GenomeLoc(dic.getSequence(seqLoc).getSequenceIndex(), nextStart, nextStart + proposedSize - 1);
+            mLoc = GenomeLocParser.createGenomeLoc(dic.getSequence(seqLoc).getSequenceIndex(), nextStart, nextStart + proposedSize - 1);
             return LocusShard.toShard(mLoc);
         }
         // else we can't make it in the current location, we have to stitch one together
@@ -207,7 +208,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
 
             // move to the next contig
             // the next sequence should start at the begining of the next contig
-            Shard ret = LocusShard.toShard(new GenomeLoc(dic.getSequence(seqLoc).getSequenceIndex(), nextStart, nextStart + lastGenomeLocSize - 1));
+            Shard ret = LocusShard.toShard(GenomeLocParser.createGenomeLoc(dic.getSequence(seqLoc).getSequenceIndex(), nextStart, nextStart + lastGenomeLocSize - 1));
 
             // now  jump ahead to the next contig
             jumpContig();
@@ -226,7 +227,7 @@ public abstract class LocusShardStrategy implements ShardStrategy {
             return;
         }
         logger.debug("Next contig, index = " + dic.getSequence(seqLoc).getSequenceIndex());
-        mLoc = new GenomeLoc(dic.getSequence(seqLoc).getSequenceIndex(), 0, 0);
+        mLoc = GenomeLocParser.createGenomeLoc(dic.getSequence(seqLoc).getSequenceIndex(), 0, 0);
 
 
     }

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

@@ -14,6 +14,7 @@ import org.broadinstitute.sting.gatk.Reads;
 import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -184,7 +185,7 @@ public class SAMDataSource implements SimpleDataSource {
 
         if (!intoUnmappedReads) {
             if (lastReadPos == null) {
-                lastReadPos = new GenomeLoc(getHeader().getSequenceDictionary().getSequence(0).getSequenceIndex(), 0, Integer.MAX_VALUE);
+                lastReadPos = GenomeLocParser.createGenomeLoc(getHeader().getSequenceDictionary().getSequence(0).getSequenceIndex(), 0, Integer.MAX_VALUE);
                 iter = iteratorPool.iterator(lastReadPos);
                 return InitialReadIterator(shard.getSize(), iter);
             } else {
@@ -280,7 +281,8 @@ public class SAMDataSource implements SimpleDataSource {
                 ++x;
             } else {
                 // jump contigs
-                if (lastReadPos.toNextContig() == false) {
+                lastReadPos = GenomeLocParser.toNextContig(lastReadPos);
+                if (lastReadPos == null) {
                     // check to see if we're using unmapped reads, if not return, we're done
                     readsTaken = 0;
                     intoUnmappedReads = true;
@@ -304,7 +306,7 @@ public class SAMDataSource implements SimpleDataSource {
         else if (rec != null) {
             int stopPos = rec.getAlignmentStart();
             if (stopPos < lastReadPos.getStart()) {
-                lastReadPos = new GenomeLoc(lastReadPos.getContigIndex() + 1, stopPos, stopPos);
+                lastReadPos = GenomeLocParser.createGenomeLoc(lastReadPos.getContigIndex() + 1, stopPos, stopPos);
             } else {
                 lastReadPos.setStart(rec.getAlignmentStart());
             }

java/src/org/broadinstitute/sting/gatk/executive/MicroScheduler.java

@@ -18,9 +18,9 @@ import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.Reads;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 
 import java.io.File;
@@ -202,7 +202,7 @@ public abstract class MicroScheduler {
         catch (FileNotFoundException ex) {
             throw new StingException("I/O error while opening fasta file: " + ex.getMessage(), ex);
         }
-        GenomeLoc.setupRefContigOrdering(ref);
+        GenomeLocParser.setupRefContigOrdering(ref);
         return ref;
     }
 }

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

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.iterators;
 
-import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.NoSuchElementException;
 /**
@@ -39,7 +39,7 @@ public class GenomeLocusIterator implements LocusIterator {
      */
     public GenomeLocusIterator( GenomeLoc completeLocus ) {
         this.completeLocus = completeLocus;
-        this.currentLocus = new GenomeLoc(completeLocus.getContig(),completeLocus.getStart());
+        this.currentLocus = GenomeLocParser.createGenomeLoc(completeLocus.getContig(),completeLocus.getStart());
     }
 
     /**

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

@@ -1,15 +1,16 @@
 package org.broadinstitute.sting.gatk.iterators;
 
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.AlignmentBlock;
-import org.broadinstitute.sting.utils.*;
+import net.sf.samtools.SAMRecord;
+import org.apache.log4j.Logger;
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.RefHanger;
+import org.broadinstitute.sting.utils.Utils;
 
 import java.util.Iterator;
 
-import org.broadinstitute.sting.utils.RefHanger;
-import org.broadinstitute.sting.gatk.LocusContext;
-import org.apache.log4j.Logger;
-
 /**
  * Iterator that traverses a SAM File, accumulating information on a per-locus basis
  */
@@ -103,12 +104,12 @@ public class LocusContextIteratorByHanger extends LocusContextIterator {
     }
 
     protected void hangRead(final SAMRecord read) {
-        GenomeLoc readLoc = new GenomeLoc(read);
+        GenomeLoc readLoc = GenomeLocParser.createGenomeLoc(read);
 
         for ( AlignmentBlock block : read.getAlignmentBlocks() ) {
             if ( DEBUG ) logger.debug(String.format("Processing block %s len=%d", block, block.getLength()));
             for ( int i = 0; i < block.getLength(); i++ ) {
-                GenomeLoc offset = new GenomeLoc(readLoc.getContigIndex(), block.getReferenceStart() + i);
+                GenomeLoc offset = GenomeLocParser.createGenomeLoc(readLoc.getContigIndex(), block.getReferenceStart() + i);
                 readHanger.expandingPut(offset, read);
                 offsetHanger.expandingPut(offset, block.getReadStart() + i - 1);
                 if ( DEBUG ) logger.debug(String.format("  # Added %s", offset));
@@ -134,7 +135,7 @@ public class LocusContextIteratorByHanger extends LocusContextIterator {
             return true;
         else {
             final SAMRecord read = it.peek();
-            GenomeLoc readLoc = new GenomeLoc(read);
+            GenomeLoc readLoc = GenomeLocParser.createGenomeLoc(read);
             final boolean coveredP = currentPositionIsFullyCovered(readLoc);
             //System.out.printf("CoverP = %s => %b%n", readLoc, coveredP);
             return coveredP;
@@ -161,7 +162,7 @@ public class LocusContextIteratorByHanger extends LocusContextIterator {
             SAMRecord read = it.next();
             justCleared = false;
 
-            GenomeLoc readLoc = new GenomeLoc(read);
+            GenomeLoc readLoc = GenomeLocParser.createGenomeLoc(read);
             if ( DEBUG ) {
                 logger.debug(String.format("  Expanding window sizes %d with %d : left=%s, right=%s, readLoc = %s, cmp=%d",
                         readHanger.size(), incrementSize,

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

@@ -5,6 +5,7 @@ import net.sf.samtools.util.RuntimeIOException;
 import net.sf.samtools.util.StringUtil;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 
 import java.util.Iterator;
@@ -65,7 +66,7 @@ public class ReferenceIterator implements Iterator<ReferenceIterator> {
     }
 
     public GenomeLoc getLocation() {
-        return new GenomeLoc(getCurrentContig().getName(), getPosition());
+        return GenomeLocParser.createGenomeLoc(getCurrentContig().getName(), getPosition());
     }
 
     // --------------------------------------------------------------------------------------------------------------
@@ -137,11 +138,11 @@ public class ReferenceIterator implements Iterator<ReferenceIterator> {
         if (seekOffset < offset  ) {  
             // bad boy -- can't go backward safely
             throw new IllegalArgumentException(String.format("Invalid seek %s => %s, which is usually due to out of order reads%n",
-                    new GenomeLoc(currentContig.getName(), offset), new GenomeLoc(seekContigName, seekOffset)));
+                    GenomeLocParser.createGenomeLoc(currentContig.getName(), offset), GenomeLocParser.createGenomeLoc(seekContigName, seekOffset)));
         } else if (seekOffset >= currentContig.length()) {
             // bad boy -- can't go beyond the contig length
             throw new IllegalArgumentException(String.format("Invalid seek to %s, which is beyond the end of the contig%n",
-                    new GenomeLoc(currentContig.getName(), seekOffset + 1)));
+                    GenomeLocParser.createGenomeLoc(currentContig.getName(), seekOffset + 1)));
         } else {
             offset = seekOffset - 1;
             return next();
@@ -160,15 +161,16 @@ public class ReferenceIterator implements Iterator<ReferenceIterator> {
         if (DEBUG)
             logger.debug(String.format("  -> Seeking to %s %d from %s %d%n", seekContigName, seekOffset, currentContig.getName(), offset));
 
-        int cmpContigs = GenomeLoc.compareContigs(seekContigName, currentContig.getName());
+
+        int cmpContigs = GenomeLocParser.compareContigs(seekContigName,currentContig.getName());
         
-        if ( cmpContigs < 0 && GenomeLoc.hasKnownContigOrdering() ) {  // if we know the order of contigs and we are already past the contig we seek, it's too late! 
+        if ( cmpContigs < 0 && GenomeLocParser.hasKnownContigOrdering() ) {  // if we know the order of contigs and we are already past the contig we seek, it's too late!
             // The contig we are looking for is before the currentContig -- it's an error
             throw new IllegalArgumentException(String.format("Invalid seek %s => %s, contigs/sequences are out of order%n",
-                    new GenomeLoc(currentContig.getName(), offset), new GenomeLoc(seekContigName, seekOffset)));
+                    GenomeLocParser.createGenomeLoc(currentContig.getName(), offset), GenomeLocParser.createGenomeLoc(seekContigName, seekOffset)));
         } 
         
-        if ( cmpContigs > 0 ||  (! GenomeLoc.hasKnownContigOrdering() ) && cmpContigs != 0 ) { // if contig we seek is still ahead, or if we have no idea what the order is and current contig is not what we seek
+        if ( cmpContigs > 0 ||  (! GenomeLocParser.hasKnownContigOrdering() ) && cmpContigs != 0 ) { // if contig we seek is still ahead, or if we have no idea what the order is and current contig is not what we seek
             // then try to seek forward in the reference file until we get the contig we need
             if (DEBUG)
                 logger.debug(String.format("  -> Seeking in the fasta file to %s from %s%n", seekContigName, currentContig.getName()));
@@ -176,7 +178,7 @@ public class ReferenceIterator implements Iterator<ReferenceIterator> {
             if (!refFile.seekToContig(seekContigName)) { // ok, do the seek
                 // a false result indicates a failure, throw a somewhat cryptic call
                 throw new RuntimeIOException(String.format("Unexpected seek failure from %s to %s%n",
-                        new GenomeLoc(currentContig.getName(), offset), new GenomeLoc(seekContigName, seekOffset)));
+                        GenomeLocParser.createGenomeLoc(currentContig.getName(), offset), GenomeLocParser.createGenomeLoc(seekContigName, seekOffset)));
             }
 
             readNextContig(); // since we haven't failed, we just read in the next contig (which is seekContigName)

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

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.iterators;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.RuntimeIOException;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.Reads;
 
 import java.util.Iterator;
@@ -63,8 +64,8 @@ public class VerifyingSamIterator implements StingSAMIterator {
         if ( last == null || cur.getReadUnmappedFlag() )
             return false;
         else {
-            GenomeLoc lastLoc = new GenomeLoc( last );
+            GenomeLoc lastLoc = GenomeLocParser.createGenomeLoc( last );
-            GenomeLoc curLoc = new GenomeLoc( cur );
+            GenomeLoc curLoc = GenomeLocParser.createGenomeLoc( cur );
             return curLoc.compareTo(lastLoc) == -1;
         }
     }

java/src/org/broadinstitute/sting/gatk/refdata/HapMapAlleleFrequenciesROD.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.List;
 import java.util.Arrays;
@@ -79,7 +80,7 @@ public class HapMapAlleleFrequenciesROD extends BasicReferenceOrderedDatum {
             varFreq = Double.parseDouble(parts[11]); // CEU_var_freq
             totalCounts = Integer.parseInt(parts[12]); // CEU_var
 
-            loc = GenomeLoc.parseGenomeLoc(contig, start, stop);
+            loc = GenomeLocParser.parseGenomeLoc(contig, start, stop);
 
         } catch ( RuntimeException e ) {
             System.out.printf("  Exception caught during parsing HapMap Allele Freq %s%n", Utils.join(" <=> ", parts));

java/src/org/broadinstitute/sting/gatk/refdata/KGenomesSNPROD.java

@@ -1,19 +1,9 @@
 package org.broadinstitute.sting.gatk.refdata;
 
 import java.util.*;
-import java.util.regex.MatchResult;
-import java.util.regex.Pattern;
-import java.util.regex.Matcher;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.IOException;
 
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.xReadLines;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
-import org.apache.log4j.Logger;
 
 /**
  * loc ref alt EM_alt_freq discovery_likelihood discovery_null discovery_prior discovery_lod EM_N n_ref n_het n_hom
@@ -28,7 +18,7 @@ public class KGenomesSNPROD extends TabularROD implements SNPCallFromGenotypes {
     }
 
     public GenomeLoc getLocation() {
-        loc = new GenomeLoc(this.get("0"), Long.parseLong(this.get("1")));
+        loc = GenomeLocParser.createGenomeLoc(this.get("0"), Long.parseLong(this.get("1")));
         return loc;
     }
     public String getRefBasesFWD() { return this.get("2"); }

java/src/org/broadinstitute/sting/gatk/refdata/SAMPileupRecord.java

@@ -6,10 +6,7 @@ import java.util.*;
 import java.util.regex.Pattern;
 import java.util.regex.Matcher;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.Pileup;
-import org.broadinstitute.sting.utils.xReadLines;
 
 import net.sf.picard.reference.ReferenceSequenceFileWalker;
 
@@ -97,8 +94,8 @@ class SAMPileupRecord implements Genotype, GenotypeList, Pileup {
 		   if ( refBaseChar == '*' ) {
  	
 			   parseIndels(observedString) ;
-			   if ( varType == DELETION_VARIANT ) loc = new GenomeLoc(contig, start, start+eventLength-1);
+			   if ( varType == DELETION_VARIANT ) loc = GenomeLocParser.createGenomeLoc(contig, start, start+eventLength-1);
-			   else loc = new GenomeLoc(contig, start, start-1); // if it's not a deletion and we are biallelic, this got to be an insertion; otherwise the state is inconsistent!!!!
+			   else loc = GenomeLocParser.createGenomeLoc(contig, start, start-1); // if it's not a deletion and we are biallelic, this got to be an insertion; otherwise the state is inconsistent!!!!
 		   } else {
 			   parseBasesAndQuals(line,pos[7]+1,pos[8], pos[8]+1, ( pos.length > 9 ? pos[9] : line.length()) );
 //			   parseBasesAndQuals(line.substring(pos[7]+1,pos[8]), line.substring(pos[8]+1, ( pos.length > 9 ? pos[9] : line.length()) ) );
@@ -108,7 +105,7 @@ class SAMPileupRecord implements Genotype, GenotypeList, Pileup {
 			   refBases = line.substring(pos[1]+1, pos[2]).toUpperCase();
 			   eventLength = 1;
 			   //loc = new GenomeLoc(contig, start, start+1);
-			   loc = new GenomeLoc(contig, start, start);
+			   loc = GenomeLocParser.createGenomeLoc(contig, start, start);
 
 			   char ch = observedString.charAt(0);
 
@@ -170,8 +167,8 @@ class SAMPileupRecord implements Genotype, GenotypeList, Pileup {
             if ( refBaseChar == '*' ) {
             	
                 parseIndels(parts[3]) ;
-                if ( varType == DELETION_VARIANT ) loc = GenomeLoc.parseGenomeLoc(contig, start, start+eventLength-1);
+                if ( varType == DELETION_VARIANT ) loc = GenomeLocParser.parseGenomeLoc(contig, start, start+eventLength-1);
-                else loc = GenomeLoc.parseGenomeLoc(contig, start, start-1); // if it's not a deletion and we are biallelic, this got to be an insertion; otherwise the state is inconsistent!!!!
+                else loc = GenomeLocParser.parseGenomeLoc(contig, start, start-1); // if it's not a deletion and we are biallelic, this got to be an insertion; otherwise the state is inconsistent!!!!
             }
             else {
                 parseBasesAndQuals(parts[8], parts[9]);
@@ -181,7 +178,7 @@ class SAMPileupRecord implements Genotype, GenotypeList, Pileup {
                 refBases = parts[2].toUpperCase();
                 eventLength = 1;
                 //loc = GenomeLoc.parseGenomeLoc(contig, start, start+1);
-                loc = GenomeLoc.parseGenomeLoc(contig, start, start);
+                loc = GenomeLocParser.parseGenomeLoc(contig, start, start);
 
                 char ch = parts[3].charAt(0);
 
@@ -623,7 +620,7 @@ class SAMPileupRecord implements Genotype, GenotypeList, Pileup {
 			System.exit(1);
 		}
 
-		GenomeLoc.setupRefContigOrdering(reference.getSequenceDictionary());
+		GenomeLocParser.setupRefContigOrdering(reference.getSequenceDictionary());
 		
 		int counter = 0;
 		

java/src/org/broadinstitute/sting/gatk/refdata/TabularROD.java

@@ -1,17 +1,16 @@
 package org.broadinstitute.sting.gatk.refdata;
 
 import java.util.*;
-import java.util.regex.MatchResult;
 import java.util.regex.Pattern;
 import java.util.regex.Matcher;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.IOException;
 
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.apache.log4j.Logger;
 
 /**
@@ -201,7 +200,7 @@ public class TabularROD extends BasicReferenceOrderedDatum implements Map<String
         String s = get(header.get(0));
         if ( s == null )
             return null;
-        return GenomeLoc.parseGenomeLoc(s);
+        return GenomeLocParser.parseGenomeLoc(s);
     }
 
     public ArrayList<String> getHeader() {

java/src/org/broadinstitute/sting/gatk/refdata/Transcript.java

@@ -5,6 +5,7 @@ import java.util.List;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 /** Holds a single transcript annotation: refseq id, gene name, genomic locations of the locus, of the coding region 
  * and of all the exons. 
@@ -75,8 +76,8 @@ public class Transcript {
 			else throw new StingException("Expected strand symbol (+/-), found: "+fields[3]);
 			
 			String contig_name = fields[2];
-			transcript_interval = GenomeLoc.parseGenomeLoc(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5]));
+			transcript_interval = GenomeLocParser.parseGenomeLoc(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5]));
-			transcript_coding_interval = GenomeLoc.parseGenomeLoc(contig_name, Integer.parseInt(fields[6])+1, Integer.parseInt(fields[7]));
+			transcript_coding_interval = GenomeLocParser.parseGenomeLoc(contig_name, Integer.parseInt(fields[6])+1, Integer.parseInt(fields[7]));
 			gene_name = fields[12];
 			String[] exon_starts = fields[9].split(",");
 			String[] exon_stops = fields[10].split(",");
@@ -89,7 +90,7 @@ public class Transcript {
 			exon_frames = new ArrayList<Integer>(eframes.length);
 			
 			for ( int i = 0 ; i < exon_starts.length  ; i++ ) {
-				exons.add(GenomeLoc.parseGenomeLoc(contig_name, Integer.parseInt(exon_starts[i])+1, Integer.parseInt(exon_stops[i]) ) );
+				exons.add(GenomeLocParser.parseGenomeLoc(contig_name, Integer.parseInt(exon_starts[i])+1, Integer.parseInt(exon_stops[i]) ) );
 				exon_frames.add(Integer.decode(eframes[i]));
 			}
 		}

java/src/org/broadinstitute/sting/gatk/refdata/rodDbSNP.java

@@ -4,10 +4,10 @@ import net.sf.picard.util.SequenceUtil;
 
 import java.util.*;
 
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.MalformedGenomeLocException;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
 
 /**
@@ -162,7 +162,7 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
             String contig = parts[1];
             long start = Long.parseLong(parts[2]) + 1; // The final is 0 based
             long stop = Long.parseLong(parts[3]) + 1;  // The final is 0 based
-            loc = GenomeLoc.parseGenomeLoc(contig, start, stop-1);
+            loc = GenomeLocParser.parseGenomeLoc(contig, start, stop-1);
 
             name = parts[4];
             refBases = parts[5];

java/src/org/broadinstitute/sting/gatk/refdata/rodGFF.java

@@ -1,15 +1,15 @@
 package org.broadinstitute.sting.gatk.refdata;
 
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.Utils;
+
 import java.util.HashMap;
-import java.util.Scanner;
 import java.util.Map;
+import java.util.Scanner;
 import java.util.regex.MatchResult;
 import java.util.regex.Pattern;
 
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
-
 /**
  * Class for representing arbitrary reference ordered data sets
  *
@@ -73,7 +73,7 @@ public class rodGFF extends BasicReferenceOrderedDatum {
     }
 
     public GenomeLoc getLocation() {
-        return GenomeLoc.parseGenomeLoc(contig, start, stop);
+        return GenomeLocParser.parseGenomeLoc(contig, start, stop);
     }
 
     public String getAttribute(final String key) {

java/src/org/broadinstitute/sting/gatk/refdata/rodRefSeq.java

@@ -13,6 +13,7 @@ import org.broadinstitute.sting.gatk.refdata.Transcript;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.xReadLines;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 public class rodRefSeq extends BasicReferenceOrderedDatum {
 
@@ -178,8 +179,8 @@ class refSeqIterator implements Iterator<rodRefSeq> {
 		
 		while ( reader.hasNext() ) {
 			Transcript t = reader.peek();
-			int ci1 = GenomeLoc.getContigIndex(curr_contig_name);
+			int ci1 = GenomeLocParser.getContigIndex(curr_contig_name);
-			int ci2 = GenomeLoc.getContigIndex( t.getLocation().getContig() ); 
+			int ci2 = GenomeLocParser.getContigIndex( t.getLocation().getContig() );
 			if ( ci1 > ci2 ) throw new StingException("RefSeq track seems to be not contig-ordered");
 			if ( ci1 < ci2 ) break; // next transcript is on the next contig, we do not need it yet...
 			if ( t.getLocation().getStart() > curr_position ) break; // next transcript is on the same contig but starts after the current position; we are done
@@ -192,7 +193,7 @@ class refSeqIterator implements Iterator<rodRefSeq> {
 		
 		// 'records' and current position are fully updated. We can now create new rod and return it (NOTE: this iterator will break if the list
 		// of pre-loaded records is meddled with by the clients between iterations, so we return them as unmodifiable list)
-		rodRefSeq rod = new rodRefSeq(name,GenomeLoc.parseGenomeLoc(curr_contig_name,curr_position, curr_position),Collections.unmodifiableList(records));
+		rodRefSeq rod = new rodRefSeq(name, GenomeLocParser.parseGenomeLoc(curr_contig_name,curr_position, curr_position),Collections.unmodifiableList(records));
 //		if ( (++z) % 1000000 == 0 ) {
 //			System.out.println(rod.getLocation()+": holding "+records.size()+ "; time per 1M ref positions: "+((double)(System.currentTimeMillis()-t)/1000.0)+" s");
 //			z = 0;

java/src/org/broadinstitute/sting/gatk/refdata/rodSAMPileup.java

@@ -7,6 +7,7 @@ import java.util.*;
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import net.sf.picard.reference.ReferenceSequenceFileWalker;
 
@@ -192,7 +193,7 @@ public class rodSAMPileup extends BasicReferenceOrderedDatum implements Genotype
 			System.exit(1);
 		}
 
-		GenomeLoc.setupRefContigOrdering(reference.getSequenceDictionary());
+		GenomeLocParser.setupRefContigOrdering(reference.getSequenceDictionary());
 		
 		int counter = 0;
 		

java/src/org/broadinstitute/sting/gatk/refdata/rodVariants.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.io.IOException;
 
@@ -22,7 +23,7 @@ public class rodVariants extends BasicReferenceOrderedDatum {
 
     public boolean parseLine(Object header, String[] parts) throws IOException {
         if (!parts[0].startsWith("#")) {
-            loc = new GenomeLoc(parts[0], Long.valueOf(parts[1]));
+            loc = GenomeLocParser.createGenomeLoc(parts[0], Long.valueOf(parts[1]));
             refBase = parts[2].charAt(0);
             depth = Integer.valueOf(parts[3]);
             maxMappingQuality = Integer.valueOf(parts[4]);

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

@@ -443,7 +443,7 @@ public abstract class TraversalEngine {
             //this.refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(refFileName);
             this.refFile = new FastaSequenceFile2(refFileName);   // todo: replace when FastaSequenceFile2 is in picard
             this.refIter = new ReferenceIterator(this.refFile);
-            if (!GenomeLoc.setupRefContigOrdering(this.refFile)) {
+            if (!GenomeLocParser.setupRefContigOrdering(this.refFile)) {
               // We couldn't process the reference contig ordering, fail since we need it
                 Utils.scareUser(String.format("We couldn't load the contig dictionary associated with %s.  At the current time we require this dictionary file to efficiently access the FASTA file.  Please use /seq/software/picard/current/bin/CreateSequenceDictionary.jar to create a sequence dictionary for your file", refFileName));
             }
@@ -470,7 +470,7 @@ public abstract class TraversalEngine {
         while (true) {
             ReferenceSequence ref = refFile.nextSequence();
             logger.debug(String.format("%s %d %d", ref.getName(), ref.length(), System.currentTimeMillis()));
-            printProgress(true, "loci", new GenomeLoc("foo", 1));
+            printProgress(true, "loci", GenomeLocParser.createGenomeLoc("foo", 1));
         }
     }
 

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

@@ -11,6 +11,7 @@ import org.broadinstitute.sting.gatk.iterators.ReferenceIterator;
 import org.broadinstitute.sting.gatk.iterators.MergingSamRecordIterator2;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.util.*;
 import java.io.File;
@@ -141,7 +142,7 @@ public class TraverseByLocusWindows extends TraversalEngine {
                 walker.nonIntervalReadAction(read);
             }
             else {
-                GenomeLoc loc = new GenomeLoc(read);
+                GenomeLoc loc = GenomeLocParser.createGenomeLoc(read);
                 // if we're in the current interval, add it to the list
                 if ( currentInterval.overlapsP(loc) ) {
                     intervalReads.add(read);
@@ -243,7 +244,7 @@ public class TraverseByLocusWindows extends TraversalEngine {
             }
         }
 
-        GenomeLoc window = new GenomeLoc(interval.getContig(), leftmostIndex, rightmostIndex);
+        GenomeLoc window = GenomeLocParser.createGenomeLoc(interval.getContig(), leftmostIndex, rightmostIndex);
         LocusContext locus = new LocusContext(window, reads, null);
         if ( DOWNSAMPLE_BY_COVERAGE )
             locus.downsampleToCoverage(downsamplingCoverage);
@@ -255,8 +256,8 @@ public class TraverseByLocusWindows extends TraversalEngine {
         GenomeLoc loc = locus1.getLocation().merge(locus2.getLocation());
         TreeSet<SAMRecord> set = new TreeSet<SAMRecord>(new Comparator<SAMRecord>() {
             public int compare(SAMRecord obj1, SAMRecord obj2) {
-                GenomeLoc myLoc = new GenomeLoc(obj1);
+                GenomeLoc myLoc = GenomeLocParser.createGenomeLoc(obj1);
-                GenomeLoc hisLoc = new GenomeLoc(obj2);
+                GenomeLoc hisLoc = GenomeLocParser.createGenomeLoc(obj2);
                 int comparison = myLoc.compareTo(hisLoc);
                  // if the reads have the same start position, we must give a non-zero comparison
                  // (because java Sets often require "consistency with equals")

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

@@ -1,25 +1,28 @@
 package org.broadinstitute.sting.gatk.traversals;
 
+import net.sf.picard.filter.FilteringIterator;
+import net.sf.picard.filter.SamRecordFilter;
 import net.sf.samtools.SAMRecord;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.LocusContext;
-import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.providers.ReadView;
+import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.shards.ReadShard;
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.DuplicateWalker;
+import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Pair;
 
 import java.io.File;
-import java.util.*;
+import java.util.ArrayList;
-
+import java.util.Arrays;
-import net.sf.picard.filter.FilteringIterator;
+import java.util.Iterator;
-import net.sf.picard.filter.SamRecordFilter;
+import java.util.List;
 
 /**
  *
@@ -66,12 +69,12 @@ public class TraverseDuplicates extends TraversalEngine {
 
     private List<SAMRecord> readsAtLoc(final SAMRecord read, PushbackIterator<SAMRecord> iter)
     {
-        GenomeLoc site = new GenomeLoc(read);
+        GenomeLoc site = GenomeLocParser.createGenomeLoc(read);
         ArrayList<SAMRecord> l = new ArrayList<SAMRecord>();
 
         l.add(read);
         for (SAMRecord read2: iter) {
-            GenomeLoc site2 = new GenomeLoc(read2);
+            GenomeLoc site2 = GenomeLocParser.createGenomeLoc(read2);
 
             // the next read starts too late
             if ( site2.getStart() != site.getStart() ) {
@@ -105,12 +108,12 @@ public class TraverseDuplicates extends TraversalEngine {
         // At this point, there are two possibilities, we have found at least one dup or not
         // if it's a dup, add it to the dups list, otherwise add it to the uniques list 
         if ( key != null ) {
-            final GenomeLoc keyLoc = new GenomeLoc(key);
+            final GenomeLoc keyLoc = GenomeLocParser.createGenomeLoc(key);
-            final GenomeLoc keyMateLoc = new GenomeLoc(key.getMateReferenceIndex(), key.getMateAlignmentStart(), key.getMateAlignmentStart());
+            final GenomeLoc keyMateLoc = GenomeLocParser.createGenomeLoc(key.getMateReferenceIndex(), key.getMateAlignmentStart(), key.getMateAlignmentStart());
 
             for ( SAMRecord read : reads ) {
-                final GenomeLoc readLoc = new GenomeLoc(read);
+                final GenomeLoc readLoc = GenomeLocParser.createGenomeLoc(read);
-                final GenomeLoc readMateLoc = new GenomeLoc(read.getMateReferenceIndex(), read.getMateAlignmentStart(), read.getMateAlignmentStart());
+                final GenomeLoc readMateLoc = GenomeLocParser.createGenomeLoc(read.getMateReferenceIndex(), read.getMateAlignmentStart(), read.getMateAlignmentStart());
                 if (DEBUG) logger.debug(String.format("Examining reads at %s vs. %s at %s / %s vs. %s / %s%n", key.getReadName(), read.getReadName(), keyLoc, keyMateLoc, readLoc, readMateLoc));
 
                 // read and key start at the same place, and either the this read and the key
@@ -150,7 +153,7 @@ public class TraverseDuplicates extends TraversalEngine {
         PushbackIterator<SAMRecord> iter = new PushbackIterator<SAMRecord>(readIter);
         for (SAMRecord read: iter) {
             // get the genome loc from the read
-            GenomeLoc site = new GenomeLoc(read);
+            GenomeLoc site = GenomeLocParser.createGenomeLoc(read);
             List<SAMRecord> reads = readsAtLoc(read, iter);
             Pair<List<SAMRecord>, List<SAMRecord>> split = splitDuplicates(reads);
             List<SAMRecord> uniqueReads =  split.getFirst();

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

@@ -16,6 +16,7 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -121,7 +122,7 @@ public class TraverseReads extends TraversalEngine {
 
             if (needsReferenceBasesP && read.getReferenceIndex() >= 0) {
                 // get the genome loc from the read
-                GenomeLoc site = new GenomeLoc(read);
+                GenomeLoc site = GenomeLocParser.createGenomeLoc(read);
 
                 // Jump forward in the reference to this locus location
                 locus = new LocusContext(site, Arrays.asList(read), Arrays.asList(0));

java/src/org/broadinstitute/sting/playground/gatk/PrepareROD.java

@@ -1,6 +1,5 @@
 package org.broadinstitute.sting.playground.gatk;
 
-import net.sf.samtools.SAMSequenceRecord;
 import net.sf.picard.cmdline.CommandLineProgram;
 import net.sf.picard.cmdline.Usage;
 import net.sf.picard.cmdline.Option;
@@ -11,8 +10,6 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.gatk.refdata.*;
 
 import java.io.*;
-import java.util.HashMap;
-import java.util.List;
 import java.util.ArrayList;
 
 public class PrepareROD extends CommandLineProgram {
@@ -33,7 +30,7 @@ public class PrepareROD extends CommandLineProgram {
 
         // Prepare the sort ordering w.r.t. the sequence dictionary
         final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REF_FILE_ARG);
-        GenomeLoc.setupRefContigOrdering(refFile);
+        GenomeLocParser.setupRefContigOrdering(refFile);
 
         Class<? extends ReferenceOrderedDatum> rodClass = ReferenceOrderedData.Types.get(ROD_TYPE.toLowerCase()).type;
 

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

@@ -1,24 +1,20 @@
 package org.broadinstitute.sting.playground.gatk.walkers.indels;
 
-import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.cmdLine.Argument;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileReader;
 import net.sf.samtools.SAMFileWriter;
+import net.sf.samtools.SAMRecord;
 import net.sf.samtools.util.CloseableIterator;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
 
-import java.util.Map;
+import java.util.*;
-import java.util.HashMap;
-import java.util.Queue;
-import java.util.LinkedList;
-import java.util.ArrayList;
-import java.util.List;
 /**
- * User: hanna
+ * User: hanna                                                                                                                    
  * Date: Jun 10, 2009
  * Time: 2:40:19 PM
  * BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
@@ -99,7 +95,7 @@ public class CleanedReadInjector extends ReadWalker<Integer,Integer> {
      */
     @Override
     public Integer map(char[] ref, SAMRecord read) {
-        GenomeLoc loc = new GenomeLoc(read);
+        GenomeLoc loc = GenomeLocParser.createGenomeLoc(read);
 
         while( loc.isPast(interval) && intervals.size() > 0 ) {
             interval = intervals.remove();

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

@@ -18,10 +18,10 @@ 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.indels.AlignmentUtils;
 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.cmdLine.Argument;
 
 
@@ -82,7 +82,7 @@ public class IndelGenotyperWalker extends ReadWalker<Integer,Integer> {
 		
 		int nSams = getToolkit().getArguments().samFiles.size(); 
 		
-		location = new GenomeLoc(0,1);
+		location = GenomeLocParser.createGenomeLoc(0,1);
 		
 		if ( call_somatic ) {
 			if ( nSams != 2 ) {

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

@@ -4,6 +4,7 @@ import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.AlignmentBlock;
 
@@ -35,8 +36,8 @@ public class IndelIntervalWalker extends ReadWalker<IndelIntervalWalker.Interval
         long indelLeftEdge = read.getAlignmentStart() + blocks.get(0).getLength() - 1;
         long indelRightEdge = read.getAlignmentEnd() - blocks.get(blocks.size()-1).getLength() + 1;
 
-        GenomeLoc indelLoc = new GenomeLoc(read.getReferenceIndex(), indelLeftEdge, indelRightEdge);
+        GenomeLoc indelLoc = GenomeLocParser.createGenomeLoc(read.getReferenceIndex(), indelLeftEdge, indelRightEdge);
-        GenomeLoc refLoc = new GenomeLoc(read);
+        GenomeLoc refLoc = GenomeLocParser.createGenomeLoc(read);
 
         return new Interval(refLoc, indelLoc);
     }
@@ -81,7 +82,7 @@ public class IndelIntervalWalker extends ReadWalker<IndelIntervalWalker.Interval
         public Interval merge(Interval i) {
             long indelLeftEdge = Math.min(this.indelLoc.getStart(), i.indelLoc.getStart());
             long indelRightEdge = Math.max(this.indelLoc.getStop(), i.indelLoc.getStop());
-            GenomeLoc mergedIndelLoc = new GenomeLoc(this.indelLoc.getContigIndex(), indelLeftEdge, indelRightEdge);
+            GenomeLoc mergedIndelLoc = GenomeLocParser.createGenomeLoc(this.indelLoc.getContigIndex(), indelLeftEdge, indelRightEdge);
             Interval mergedInterval = new Interval(this.readLoc.merge(i.readLoc), mergedIndelLoc);
             mergedInterval.indelCount = this.indelCount + i.indelCount;
             return mergedInterval;

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

@@ -915,7 +915,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
         reads.add(r5);
         reads.add(r6);
         reads.add(r7);
-        clean(reads, reference, new GenomeLoc(0,0));
+        clean(reads, reference, GenomeLocParser.createGenomeLoc(0,0));
     }
 
     private void testCleanWithDeletion() {
@@ -971,7 +971,7 @@ public class  IntervalCleanerWalker extends LocusWindowWalker<Integer, Integer>
         reads.add(r6);
         reads.add(r7);
         reads.add(r8);
-        clean(reads, reference, new GenomeLoc(0,0));
+        clean(reads, reference, GenomeLocParser.createGenomeLoc(0,0));
     }
 
     public static String cigarToString(Cigar cig) {

java/src/org/broadinstitute/sting/playground/indels/IndelInspectorMain.java

@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.playground.indels;
 
 import java.io.File;
-import java.util.List;
 import java.util.Map;
 import java.util.HashMap;
 
@@ -16,6 +15,7 @@ import net.sf.picard.reference.ReferenceSequence;
 
 import net.sf.samtools.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 
 public class IndelInspectorMain extends CommandLineProgram {
 
@@ -55,10 +55,10 @@ public class IndelInspectorMain extends CommandLineProgram {
             System.out.println("No reference sequence dictionary found. Abort.");
         }
 
-        GenomeLoc.setupRefContigOrdering(reference.getSequenceDictionary());
+        GenomeLocParser.setupRefContigOrdering(reference.getSequenceDictionary());
         GenomeLoc location = null;
         if ( GENOME_LOCATION != null ) {
-            location = GenomeLoc.parseGenomeLoc(GENOME_LOCATION);
+            location = GenomeLocParser.parseGenomeLoc(GENOME_LOCATION);
         }
         
         if ( COUNT_CUTOFF == null ) COUNT_CUTOFF = 2;
@@ -117,8 +117,8 @@ public class IndelInspectorMain extends CommandLineProgram {
                 cur_contig = r.getReferenceName();
                 System.out.println("Contig "+cur_contig);
                 // if contig is specified and we are past that contig, we are done:
-                if ( location != null && GenomeLoc.compareContigs(cur_contig, location.getContig()) == 1 ) break;
+                if ( location != null && GenomeLocParser.compareContigs(cur_contig, location.getContig()) == 1 ) break;
-                if ( location == null || GenomeLoc.compareContigs(cur_contig, location.getContig()) == 0 ) {
+                if ( location == null || GenomeLocParser.compareContigs(cur_contig, location.getContig()) == 0 ) {
                 	if ( location != null ) System.out.println("Time spent to scroll input bam file to the specified chromosome: "+ ((System.currentTimeMillis()-tc)/1000) + " seconds.");
                 	tc = System.currentTimeMillis();
                     contig_seq = reference.get(r.getReferenceIndex());
@@ -130,7 +130,7 @@ public class IndelInspectorMain extends CommandLineProgram {
             }
 
             // if contig is specified and we did not reach it yet, skip the records until we reach that contig:
-            if ( location != null && GenomeLoc.compareContigs(cur_contig, location.getContig()) == -1 ) continue;
+            if ( location != null && GenomeLocParser.compareContigs(cur_contig, location.getContig()) == -1 ) continue;
 
             if ( location != null && r.getAlignmentEnd() < location.getStart() ) continue;
 
@@ -327,7 +327,7 @@ public class IndelInspectorMain extends CommandLineProgram {
             setDefaultContigOrdering();
             return;
         }
-        GenomeLoc.setupRefContigOrdering(h.getSequenceDictionary());
+        GenomeLocParser.setupRefContigOrdering(h.getSequenceDictionary());
     }
 
     private void setDefaultContigOrdering() {

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

@@ -1,17 +1,10 @@
 package org.broadinstitute.sting.utils;
 
-import edu.mit.broad.picard.util.Interval;
-import edu.mit.broad.picard.directed.IntervalList;
-import net.sf.picard.reference.ReferenceSequenceFile;
 import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMSequenceDictionary;
-import net.sf.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
 
-import java.io.File;
+import java.util.ArrayList;
-import java.util.*;
+import java.util.List;
-import java.util.regex.Matcher;
-import java.util.regex.Pattern;
 
 /**
  * Created by IntelliJ IDEA.
@@ -26,253 +19,49 @@ import java.util.regex.Pattern;
 public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
     private static Logger logger = Logger.getLogger(GenomeLoc.class);
 
+    /**
+     * the basic components of a genome loc, its contig index,
+     * start and stop position, and (optionally) the contig name
+     */
     private int contigIndex;
     private long start;
     private long stop;
-
+    private String contigName;
-    // --------------------------------------------------------------------------------------------------------------
+    static int MAX_CONTIG;
-    //
-    // Ugly global variable defining the optional ordering of contig elements
-    //
-    // --------------------------------------------------------------------------------------------------------------
-    //public static Map<String, Integer> refContigOrdering = null;
-    private static SAMSequenceDictionary contigInfo = null;
-
-    public static boolean hasKnownContigOrdering() {
-        return contigInfo != null;
-    }
-
-    
-    public static SAMSequenceRecord getContigInfo( final String contig ) {
-        return contigInfo.getSequence(contig);
-    }
-
-    /**
-     * Returns the contig index of a specified string version of the contig
-     * @param contig the contig string
-     * @return the contig index, -1 if not found
-     */
-    public static int getContigIndex( final String contig ) {
-        if (contigInfo.getSequenceIndex(contig) == -1)
-            Utils.scareUser(String.format("Contig %s given as location, but this contig isn't present in the Fasta sequence dictionary", contig));
-
-        return contigInfo.getSequenceIndex(contig);
-    }
-
-    public static boolean setupRefContigOrdering(final ReferenceSequenceFile refFile) {
-        return setupRefContigOrdering(refFile.getSequenceDictionary());
-    }
-
-    public static boolean setupRefContigOrdering(final SAMSequenceDictionary seqDict) {
-        if (seqDict == null)  { // we couldn't load the reference dictionary
-        	logger.info("Failed to load reference dictionary, falling back to lexicographic order for contigs");
-            Utils.scareUser("Failed to load reference dictionary");
-            return false;
-        } else if ( contigInfo == null ){
-            contigInfo = seqDict;
-            logger.debug(String.format("Prepared reference sequence contig dictionary"));
-            for (SAMSequenceRecord contig : seqDict.getSequences() ) {
-                logger.debug(String.format(" %s (%d bp)", contig.getSequenceName(), contig.getSequenceLength()));
-            }
-        }
-        
-        return true;
-    }
 
     // --------------------------------------------------------------------------------------------------------------
     //
     // constructors
     //
     // --------------------------------------------------------------------------------------------------------------
-    public GenomeLoc( int contigIndex, final long start, final long stop ) {
+    /*GenomeLoc( int contigIndex, final long start, final long stop ) {
-        if(contigInfo == null) {  throw new StingException("Contig info has not been setup in the GenomeLoc context yet."); }
+        MAX_CONTIG = Integer.MAX_VALUE;
-
-        if (!isSequenceIndexValid(contigIndex)) {
-            throw new StingException("Contig info has not been setup in the GenomeLoc context yet.");
-        }
         if (start < 0) { throw new StingException("Bad start position " + start);}
         if (stop  < -1) { throw new StingException("Bad stop position " + stop); }    // a negative -1 indicates it's not a meaningful end position
 
         this.contigIndex = contigIndex;
         this.start = start;
+        this.contigName = null;  // we just don't know
         this.stop = stop == -1 ? start : stop;
+    }*/
+
+    GenomeLoc(final SAMRecord read) {
+        this(read.getHeader().getSequence(read.getReferenceIndex()).getSequenceName(), read.getReferenceIndex(), read.getAlignmentStart(), read.getAlignmentEnd());
     }
 
-    public GenomeLoc(final SAMRecord read) {
+    GenomeLoc( final String contig, final int contigIndex, final long start, final long stop ) {
-        this(read.getReferenceIndex(), read.getAlignmentStart(), read.getAlignmentEnd());
+        this.contigName = contig;
+        this.contigIndex = contigIndex;
+        this.start = start;
+        this.stop = stop;
     }
 
-    public GenomeLoc( final String contig, final long start, final long stop ) {
+    /*GenomeLoc( final int contig, final long pos ) {
-        this(contigInfo.getSequenceIndex(contig), start, stop);
-    }
-
-    public GenomeLoc( final String contig, final long pos ) {
-        this(contig, pos, pos);
-    }
-
-    public GenomeLoc( final int contig, final long pos ) {
         this(contig, pos, pos );
     }
-
+    */
-    public GenomeLoc( final GenomeLoc toCopy ) {
+    GenomeLoc( final GenomeLoc toCopy ) {
-        this( toCopy.contigIndex, toCopy.getStart(), toCopy.getStop() );
+        this( toCopy.getContig(), toCopy.contigIndex, toCopy.getStart(), toCopy.getStop() );
-    }
-
-    // --------------------------------------------------------------------------------------------------------------
-    //
-    // Parsing string representations
-    //
-    // --------------------------------------------------------------------------------------------------------------
-    private static long parsePosition( final String pos ) {
-        String x = pos.replaceAll(",", "");
-        return Long.parseLong(x);
-    }
-
-    /**
-     * Use this static constructor when the input data is under limited control (i.e. parsing user data).
-     * @param contig Contig to parse.
-     * @param start Starting point.
-     * @param stop Stop point.
-     * @return The genome location, or a MalformedGenomeLocException if unparseable.
-     */
-    public static GenomeLoc parseGenomeLoc( final String contig, long start, long stop ) {
-        if( !isContigValid(contig) )
-            throw new MalformedGenomeLocException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference.");
-        return new GenomeLoc(contig,start,stop);
-    }
-
-    public static GenomeLoc parseGenomeLoc( final String str ) {
-        // 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
-        //System.out.printf("Parsing location '%s'%n", str);
-
-        final Pattern regex1 = Pattern.compile("([\\w&&[^:]]+)$");                      // matches case 1
-        final Pattern regex2 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)$");            // matches case 2
-        final Pattern regex3 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)-([\\d,]+)$");  // matches case 3
-        final Pattern regex4 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)\\+");          // matches case 4
-
-        String contig = null;
-        long start = 1;
-        long stop = Integer.MAX_VALUE;
-        boolean bad = false;
-
-        Matcher match1 = regex1.matcher(str);
-        Matcher match2 = regex2.matcher(str);
-        Matcher match3 = regex3.matcher(str);
-        Matcher match4 = regex4.matcher(str);
-
-        try {
-            if ( match1.matches() ) {
-                contig = match1.group(1);
-            }
-            else if ( match2.matches() ) {
-                contig = match2.group(1);
-                start = parsePosition(match2.group(2));
-                stop = start;                
-            }
-            else if ( match4.matches() ) {
-                contig = match4.group(1);
-                start = parsePosition(match4.group(2));
-            }
-            else if ( match3.matches() ) {
-                contig = match3.group(1);
-                start = parsePosition(match3.group(2));
-                stop = parsePosition(match3.group(3));
-
-                if ( start > stop )
-                    bad = true;
-            }
-            else {
-                bad = true;
-            }
-        } catch ( Exception e ) {
-            bad = true;
-        }
-
-        if ( bad ) {
-            throw new StingException("Invalid Genome Location string: " + str);
-        }
-
-        if ( stop == Integer.MAX_VALUE && hasKnownContigOrdering() ) {
-            // lookup the actually stop position!
-            stop = getContigInfo(contig).getSequenceLength();
-        }
-
-        if( !isContigValid(contig) )
-            throw new MalformedGenomeLocException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference.");
-
-        GenomeLoc loc = parseGenomeLoc(contig,start,stop);
- //       System.out.printf("  => Parsed location '%s' into %s%n", str, loc);
-
-        return loc;
-    }
-
-    /**
-     * Useful utility function that parses a location string into a coordinate-order sorted
-     * array of GenomeLoc objects
-     *
-     * @param str String representation of genome locs.  Null string corresponds to no filter.
-     * @return Array of GenomeLoc objects corresponding to the locations in the string, sorted by coordinate order
-     */
-    public static List<GenomeLoc> parseGenomeLocs(final String str) {
-        // Null string means no filter.
-        if( str == null ) return null;
-
-        // Of the form: loc1;loc2;...
-        // Where each locN can be:
-        // 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
-        try {
-            List<GenomeLoc> locs = new ArrayList<GenomeLoc>();
-            for( String loc: str.split(";") )
-                locs.add( parseGenomeLoc(loc.trim()) );
-            Collections.sort(locs);
-            //logger.info(String.format("Going to process %d locations", locs.length));
-            locs = mergeOverlappingLocations(locs);
-            logger.debug("Locations are:" + Utils.join(", ", locs));
-            return locs;
-        } catch (Exception e) {
-            e.printStackTrace();
-            Utils.scareUser(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));
-            return null;
-        }
-    }
-
-    public static List<GenomeLoc> mergeOverlappingLocations(final List<GenomeLoc> raw) {
-        logger.debug("  Raw locations are:\n" + Utils.join("\n", raw));        
-        if ( raw.size() <= 1 )
-            return raw;
-        else {
-            ArrayList<GenomeLoc> merged = new ArrayList<GenomeLoc>();
-            Iterator<GenomeLoc> it = raw.iterator();
-            GenomeLoc prev = it.next();
-            while ( it.hasNext() ) {
-                GenomeLoc curr = it.next();
-                if ( prev.contiguousP(curr) ) {
-                    prev = prev.merge(curr);
-                } else {
-                    merged.add(prev);
-                    prev = curr;
-                }
-            }
-            merged.add(prev);
-            return merged;
-        }
-    }
-
-
-    /**
-     * Move this Genome loc to the next contig, with a start
-     * and stop of 1.
-     * @return true if we are not out of contigs, otherwise false if we're
-     *          at the end of the genome (no more contigs to jump to).
-     */
-    public boolean toNextContig() {
-        if ((contigIndex + 1) < GenomeLoc.contigInfo.size()) {
-            this.contigIndex++;
-            this.start = 1;
-            this.stop = 1;
-            return true;
-        }
-        return false;
     }
 
 
@@ -319,7 +108,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
             return returnTrueIfEmpty;
 
         // skip loci before intervals begin
-        if ( hasKnownContigOrdering() && curr.contigIndex < locs.get(0).contigIndex )
+        if ( curr.contigIndex < locs.get(0).contigIndex )
             return false;
 
         for ( GenomeLoc loc : locs ) {
@@ -336,23 +125,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
     // Accessors and setters
     //
     public final String getContig() {
-        //this.contigIndex != -1;
+        return this.contigName;
-        if (!(contigInfo != null && contigInfo.getSequences() != null)) {
-            throw new StingException("The contig information or it's sequences are null");
-        }
-        if ((this.contigIndex < 0) || (this.contigIndex >= contigInfo.getSequences().size())) {
-            throw new StingException("The contig index is not bounded by the zero and seqeunce count, contig index: " + contigIndex);
-        }
-        if (contigInfo.getSequence(this.contigIndex) == null ||
-            contigInfo.getSequence(this.contigIndex).getSequenceName() == null) {
-            throw new StingException("The associated sequence index for contig " + contigIndex + " is null");
-        }
-        return contigInfo.getSequence(this.contigIndex).getSequenceName();
-        //if (contigInfo != null && contigInfo.getSequence(this.contigIndex) != null) {
-        //    return contigInfo.getSequence(this.contigIndex).getSequenceName();
-        //}
-
-        //return null;
     }
 
     public final int getContigIndex() { return this.contigIndex; }
@@ -372,7 +145,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
     public final boolean atBeginningOfContigP() { return this.start == 1; }
 
     public void setContig(String contig) {
-        this.contigIndex = contigInfo.getSequenceIndex(contig);
+        this.contigName = contig;
     }
 
     public void setStart(long start) {
@@ -411,7 +184,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
             throw new StingException("The two genome loc's need to be contigous");
         }
 
-        return new GenomeLoc(getContig(),
+        return new GenomeLoc(getContig(), this.contigIndex,
                              Math.min(getStart(), that.getStart()),
                              Math.max( getStop(), that.getStop()) );
     }
@@ -497,54 +270,11 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
         return new GenomeLoc(this);
     }
 
-    //
+    /**
-    // Comparison operations
+     * conpare this genomeLoc's contig to another genome loc
-    //
+     * @param that
-    // TODO: get rid of this method because it's sloooooooooooooow
+     * @return
-    @Deprecated
+     */
-    public static int compareContigs( final String thisContig, final String thatContig )
-    {
-        if ( thisContig == thatContig )
-        {
-            // Optimization.  If the pointers are equal, then the contigs are equal.
-            return 0;
-        }
-
-        if ( hasKnownContigOrdering() )
-        {
-            int thisIndex = getContigIndex(thisContig);
-            int thatIndex = getContigIndex(thatContig);
-
-            if ( thisIndex == -1 )
-            {
-                if ( thatIndex == -1 )
-                {
-                    // Use regular sorted order
-                    return thisContig.compareTo(thatContig);
-                }
-                else
-                {
-                    // this is always bigger if that is in the key set
-                    return 1;
-                }
-            }
-            else if ( thatIndex == -1 )
-            {
-                return -1;
-            }
-            else
-            {
-                if ( thisIndex < thatIndex ) return -1;
-                if ( thisIndex > thatIndex ) return 1;
-                return 0;
-            }
-        }
-        else
-        {
-            return thisContig.compareTo(thatContig);
-        }
-    }
-
     public final int compareContigs( GenomeLoc that ) {
         if (this.contigIndex == that.contigIndex)
             return 0;
@@ -570,64 +300,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
     }
 
 
-    /**
-     * Read a file of genome locations to process.
-     * regions specified by the location string.  The string is of the form:
-     * Of the form: loc1;loc2;...
-     * Where each locN can be:
-     * 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
-     *
-     * @param file_name
-     */
-    public static List<GenomeLoc> IntervalFileToList(final String file_name) {
-// first try to read it as an interval file since that's well structured
-        // we'll fail quickly if it's not a valid file.  Then try to parse it as
-        // a location string file
-        List<GenomeLoc> ret = null;
-        try {
-            IntervalList il = IntervalList.fromFile(new File(file_name));
 
-            // iterate through the list of merged intervals and add then as GenomeLocs
-            ret = new ArrayList<GenomeLoc>();
-            for(Interval interval : il.getUniqueIntervals()) {
-                ret.add(new GenomeLoc(interval.getSequence(), interval.getStart(), interval.getEnd()));
-            }
-            return ret;
 
-        } catch (Exception e) {
-            try {
-                xReadLines reader = new xReadLines(new File(file_name));
-                List<String> lines = reader.readLines();
-                reader.close();
-                String locStr = Utils.join(";", lines);
-                logger.debug("locStr: " + locStr);
-                ret = parseGenomeLocs(locStr);
-                return ret;
-            } catch (Exception e2) {
-            	logger.error("Attempt to parse interval file in GATK format failed: "+e2.getMessage());
-                e2.printStackTrace();
-                throw new StingException("Unable to parse out interval file in either format", e);
-            }
-        }
-    }
 
-    /**
-     * Determines whether the given contig is valid with respect to the sequence dictionary
-     * already installed in the GenomeLoc.
-     * @return True if the contig is valid.  False otherwise.
-     */
-    private static boolean isContigValid( String contig ) {
-        int contigIndex = contigInfo.getSequenceIndex(contig);
-        return isSequenceIndexValid(contigIndex);
-    }
-
-    /**
-     * Determines whether the given sequence index is valid with respect to the sequence dictionary.
-     * @param sequenceIndex sequence index
-     * @return True if the sequence index is valid, false otherwise.
-     */
-    private static boolean isSequenceIndexValid( int sequenceIndex ) {
-        return sequenceIndex >= 0 && sequenceIndex < contigInfo.size();
-
-    }
 }

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

@@ -0,0 +1,484 @@
+package org.broadinstitute.sting.utils;
+
+import edu.mit.broad.picard.directed.IntervalList;
+import edu.mit.broad.picard.util.Interval;
+import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.samtools.SAMRecord;
+import net.sf.samtools.SAMSequenceDictionary;
+import net.sf.samtools.SAMSequenceRecord;
+import org.apache.log4j.Logger;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+/**
+ * Created by IntelliJ IDEA.
+ * User: aaronmckenna
+ * Date: Jun 18, 2009
+ * Time: 11:17:01 PM
+ * To change this template use File | Settings | File Templates.
+ */
+public class GenomeLocParser {
+    private static Logger logger = Logger.getLogger(GenomeLocParser.class);
+
+
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // Ugly global variable defining the optional ordering of contig elements
+    //
+    // --------------------------------------------------------------------------------------------------------------
+    //public static Map<String, Integer> refContigOrdering = null;
+    private static SAMSequenceDictionary contigInfo = null;
+
+    /**
+     * do we have a contig ordering setup?
+     *
+     * @return true if the contig order is setup
+     */
+    public static boolean hasKnownContigOrdering() {
+        return contigInfo != null;
+    }
+
+    /**
+     * get the contig's SAMSequenceRecord
+     *
+     * @param contig the string name of the contig
+     *
+     * @return the sam sequence record
+     */
+    public static SAMSequenceRecord getContigInfo(final String contig) {
+        return contigInfo.getSequence(contig);
+    }
+
+    /**
+     * Returns the contig index of a specified string version of the contig
+     *
+     * @param contig the contig string
+     *
+     * @return the contig index, -1 if not found
+     */
+    public static int getContigIndex(final String contig) {
+        if (contigInfo.getSequenceIndex(contig) == -1)
+            Utils.scareUser(String.format("Contig %s given as location, but this contig isn't present in the Fasta sequence dictionary", contig));
+
+        return contigInfo.getSequenceIndex(contig);
+    }
+
+    /**
+     * set our internal reference contig order
+     *
+     * @param refFile the reference file
+     *
+     * @return true if we were successful
+     */
+    public static boolean setupRefContigOrdering(final ReferenceSequenceFile refFile) {
+        return setupRefContigOrdering(refFile.getSequenceDictionary());
+    }
+
+    /**
+     * setup our internal reference contig order
+     *
+     * @param seqDict the sequence dictionary
+     *
+     * @return true if we were successful
+     */
+    public static boolean setupRefContigOrdering(final SAMSequenceDictionary seqDict) {
+        if (seqDict == null) { // we couldn't load the reference dictionary
+            logger.info("Failed to load reference dictionary, falling back to lexicographic order for contigs");
+            Utils.scareUser("Failed to load reference dictionary");
+            return false;
+        } else if (contigInfo == null) {
+            contigInfo = seqDict;
+            logger.debug(String.format("Prepared reference sequence contig dictionary"));
+            for (SAMSequenceRecord contig : seqDict.getSequences()) {
+                logger.debug(String.format(" %s (%d bp)", contig.getSequenceName(), contig.getSequenceLength()));
+            }
+        }
+        GenomeLoc.MAX_CONTIG = contigInfo.getSequences().size();
+        return true;
+    }
+
+    /**
+     * parse a genome location, from a location string
+     *
+     * @param str the string to parse
+     *
+     * @return a GenomeLoc representing the String
+     */
+    public static GenomeLoc parseGenomeLoc(final String str) {
+        // 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
+        //System.out.printf("Parsing location '%s'%n", str);
+
+        final Pattern regex1 = Pattern.compile("([\\w&&[^:]]+)$");                      // matches case 1
+        final Pattern regex2 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)$");            // matches case 2
+        final Pattern regex3 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)-([\\d,]+)$");  // matches case 3
+        final Pattern regex4 = Pattern.compile("([\\w&&[^:]]+):([\\d,]+)\\+");          // matches case 4
+
+        String contig = null;
+        long start = 1;
+        long stop = Integer.MAX_VALUE;
+        boolean bad = false;
+
+        Matcher match1 = regex1.matcher(str);
+        Matcher match2 = regex2.matcher(str);
+        Matcher match3 = regex3.matcher(str);
+        Matcher match4 = regex4.matcher(str);
+
+        try {
+            if (match1.matches()) {
+                contig = match1.group(1);
+            } else if (match2.matches()) {
+                contig = match2.group(1);
+                start = parsePosition(match2.group(2));
+                stop = start;
+            } else if (match4.matches()) {
+                contig = match4.group(1);
+                start = parsePosition(match4.group(2));
+            } else if (match3.matches()) {
+                contig = match3.group(1);
+                start = parsePosition(match3.group(2));
+                stop = parsePosition(match3.group(3));
+
+                if (start > stop)
+                    bad = true;
+            } else {
+                bad = true;
+            }
+        } catch (Exception e) {
+            bad = true;
+        }
+
+        if (bad) {
+            throw new StingException("Invalid Genome Location string: " + str);
+        }
+
+        if (stop == Integer.MAX_VALUE && hasKnownContigOrdering()) {
+            // lookup the actually stop position!
+            stop = getContigInfo(contig).getSequenceLength();
+        }
+
+        if (!isContigValid(contig))
+            throw new MalformedGenomeLocException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference.");
+
+        GenomeLoc loc = parseGenomeLoc(contig, start, stop);
+        //       System.out.printf("  => Parsed location '%s' into %s%n", str, loc);
+
+        return loc;
+    }
+
+    /**
+     * Useful utility function that parses a location string into a coordinate-order sorted
+     * array of GenomeLoc objects
+     *
+     * @param str String representation of genome locs.  Null string corresponds to no filter.
+     *
+     * @return Array of GenomeLoc objects corresponding to the locations in the string, sorted by coordinate order
+     */
+    public static List<GenomeLoc> parseGenomeLocs(final String str) {
+        // Null string means no filter.
+        if (str == null) return null;
+
+        // Of the form: loc1;loc2;...
+        // Where each locN can be:
+        // 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
+        try {
+            List<GenomeLoc> locs = new ArrayList<GenomeLoc>();
+            for (String loc : str.split(";"))
+                locs.add(parseGenomeLoc(loc.trim()));
+            Collections.sort(locs);
+            //logger.info(String.format("Going to process %d locations", locs.length));
+            locs = mergeOverlappingLocations(locs);
+            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);
+        }
+    }
+
+    // --------------------------------------------------------------------------------------------------------------
+    //
+    // Parsing string representations
+    //
+    // --------------------------------------------------------------------------------------------------------------
+    private static long parsePosition(final String pos) {
+        String x = pos.replaceAll(",", "");
+        return Long.parseLong(x);
+    }
+
+
+    /**
+     * merge a list of genome locs that may be overlapping, returning the list of unique genomic locations
+     *
+     * @param raw the unchecked genome loc list
+     *
+     * @return the list of merged locations
+     */
+    public static List<GenomeLoc> mergeOverlappingLocations(final List<GenomeLoc> raw) {
+        logger.debug("  Raw locations are:\n" + Utils.join("\n", raw));
+        if (raw.size() <= 1)
+            return raw;
+        else {
+            ArrayList<GenomeLoc> merged = new ArrayList<GenomeLoc>();
+            Iterator<GenomeLoc> it = raw.iterator();
+            GenomeLoc prev = it.next();
+            while (it.hasNext()) {
+                GenomeLoc curr = it.next();
+                if (prev.contiguousP(curr)) {
+                    prev = prev.merge(curr);
+                } else {
+                    merged.add(prev);
+                    prev = curr;
+                }
+            }
+            merged.add(prev);
+            return merged;
+        }
+    }
+
+    /**
+     * Determines whether the given contig is valid with respect to the sequence dictionary
+     * already installed in the GenomeLoc.
+     *
+     * @return True if the contig is valid.  False otherwise.
+     */
+    private static boolean isContigValid(String contig) {
+        int contigIndex = contigInfo.getSequenceIndex(contig);
+        return isSequenceIndexValid(contigIndex);
+    }
+
+    /**
+     * Determines whether the given sequence index is valid with respect to the sequence dictionary.
+     *
+     * @param sequenceIndex sequence index
+     *
+     * @return True if the sequence index is valid, false otherwise.
+     */
+    private static boolean isSequenceIndexValid(int sequenceIndex) {
+        return sequenceIndex >= 0 && sequenceIndex < contigInfo.size();
+
+    }
+
+    /**
+     * Use this static constructor when the input data is under limited control (i.e. parsing user data).
+     *
+     * @param contig Contig to parse.
+     * @param start  Starting point.
+     * @param stop   Stop point.
+     *
+     * @return The genome location, or a MalformedGenomeLocException if unparseable.
+     */
+    public static GenomeLoc parseGenomeLoc(final String contig, long start, long stop) {
+        if (!isContigValid(contig))
+            throw new MalformedGenomeLocException("Contig " + contig + " does not match any contig in the GATK sequence dictionary derived from the reference.");
+        return new GenomeLoc(contig, getContigIndex(contig), start, stop);
+    }
+
+
+    /**
+     * Read a file of genome locations to process.
+     * regions specified by the location string.  The string is of the form:
+     * Of the form: loc1;loc2;...
+     * Where each locN can be:
+     * 'chr2', 'chr2:1000000' or 'chr2:1,000,000-2,000,000'
+     *
+     * @param file_name
+     */
+    public static List<GenomeLoc> intervalFileToList(final String file_name) {
+        /**
+         * first try to read it as an interval file since that's well structured
+         * we'll fail quickly if it's not a valid file.  Then try to parse it as
+         * a location string file
+         */
+        List<GenomeLoc> ret = null;
+        try {
+            IntervalList il = IntervalList.fromFile(new File(file_name));
+
+            // iterate through the list of merged intervals and add then as GenomeLocs
+            ret = new ArrayList<GenomeLoc>();
+            for (Interval interval : il.getUniqueIntervals()) {
+                ret.add(new GenomeLoc(interval.getSequence(), getContigIndex(interval.getSequence()), interval.getStart(), interval.getEnd()));
+            }
+            return ret;
+
+        } catch (Exception e) {
+            try {
+                xReadLines reader = new xReadLines(new File(file_name));
+                List<String> lines = reader.readLines();
+                reader.close();
+                String locStr = Utils.join(";", lines);
+                logger.debug("locStr: " + locStr);
+                ret = parseGenomeLocs(locStr);
+                return ret;
+            } catch (Exception e2) {
+                logger.error("Attempt to parse interval file in GATK format failed: " + e2.getMessage());
+                e2.printStackTrace();
+                throw new StingException("Unable to parse out interval file in either format", e);
+            }
+        }
+    }
+
+    /**
+     * get the sequence name from a sequence index
+     *
+     * @param contigIndex get the contig index
+     *
+     * @return the string that represents that contig name
+     */
+    private static String getSequenceNameFromIndex(int contigIndex) {
+        return GenomeLocParser.contigInfo.getSequence(contigIndex).getSequenceName();
+    }
+
+    /**
+     * create a genome loc, given the contig name, start, and stop
+     *
+     * @param contig the contig name
+     * @param start  the starting position
+     * @param stop   the stop position
+     *
+     * @return a new genome loc
+     */
+    public static GenomeLoc createGenomeLoc(String contig, final long start, final long stop) {
+        checkSetup();
+        return verifyGenomeLoc(new GenomeLoc(contig, GenomeLocParser.getContigIndex(contig), start, stop));
+    }
+
+    /**
+     * create a genome loc, given the contig index, start, and stop
+     *
+     * @param contigIndex the contig index
+     * @param start       the start position
+     * @param stop        the stop position
+     *
+     * @return a new genome loc
+     */
+    public static GenomeLoc createGenomeLoc(int contigIndex, final long start, final long stop) {
+        checkSetup();
+        if (start < 0) {
+            throw new StingException("Bad start position " + start);
+        }
+        if (stop < -1) {
+            throw new StingException("Bad stop position " + stop);
+        }    // a negative -1 indicates it's not a meaningful end position
+
+
+        return new GenomeLoc(getSequenceNameFromIndex(contigIndex), contigIndex, start, stop);
+    }
+
+    /**
+     * create a genome loc, given a read
+     *
+     * @param read
+     *
+     * @return
+     */
+    public static GenomeLoc createGenomeLoc(final SAMRecord read) {
+        checkSetup();
+        return verifyGenomeLoc(new GenomeLoc(read.getReferenceName(), read.getReferenceIndex(), read.getAlignmentStart(), read.getAlignmentEnd()));
+    }
+
+
+    /**
+     * create a new genome loc, given the contig position, and a single position
+     *
+     * @param contig the contig name
+     * @param pos    the postion
+     *
+     * @return a genome loc representing a single base at the specified postion on the contig
+     */
+    public static GenomeLoc createGenomeLoc(final int contig, final long pos) {
+        checkSetup();
+        return verifyGenomeLoc(new GenomeLoc(getSequenceNameFromIndex(contig), contig, pos, pos));
+    }
+
+    /**
+     * create a new genome loc, given the contig name, and a single position
+     *
+     * @param contig the contig name
+     * @param pos    the postion
+     *
+     * @return a genome loc representing a single base at the specified postion on the contig
+     */
+    public static GenomeLoc createGenomeLoc(final String contig, final long pos) {
+        checkSetup();
+        return verifyGenomeLoc(new GenomeLoc(contig, GenomeLocParser.getContigIndex(contig), pos, pos));
+    }
+
+    public static GenomeLoc createGenomeLoc(final GenomeLoc toCopy) {
+        checkSetup();
+        return verifyGenomeLoc(new GenomeLoc(toCopy.getContig(), toCopy.getContigIndex(), toCopy.getStart(), toCopy.getStop()));
+    }
+
+    /**
+     * verify the specified genome loc is valid, if it's not, throw an exception
+     *
+     * @param toReturn teh genome loc we're about to return
+     *
+     * @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) {
+            throw new StingException("Parameters to GenomeLocParser are incorrect: the stop position is less than 0");
+        }
+        if (toReturn.getContigIndex() < 0) {
+            throw new StingException("Parameters to GenomeLocParser are incorrect: the contig index is less than 0");
+        }
+        if (toReturn.getContigIndex() >= contigInfo.getSequences().size()) {
+            throw new StingException("Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count");
+
+        }
+        return toReturn;
+
+    }
+
+
+    /**
+     * Move this Genome loc to the next contig, with a start
+     * and stop of 1.
+     *
+     * @return true if we are not out of contigs, otherwise false if we're
+     *         at the end of the genome (no more contigs to jump to).
+     */
+    public static GenomeLoc toNextContig(GenomeLoc current) {
+        if (current.getContigIndex() + 1 >= contigInfo.getSequences().size()) {
+            return null;
+        } else
+            return verifyGenomeLoc(new GenomeLoc(getSequenceNameFromIndex(current.getContigIndex() + 1), current.getContigIndex() + 1, 1, 1));
+    }
+
+    /**
+     * 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");
+        }
+    }
+
+    /**
+     * compare two contig names, in the current context
+     *
+     * @param firstContig
+     * @param secondContig
+     *
+     * @return
+     */
+    public static int compareContigs(String firstContig, String secondContig) {
+        checkSetup();
+        Integer ref1 = GenomeLocParser.getContigIndex(firstContig);
+        Integer ref2 = GenomeLocParser.getContigIndex(secondContig);
+        return ref1.compareTo(ref2);
+
+    }
+}

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

@@ -168,8 +168,8 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
                      * |------|  + |--------|
                      *
                      */
-                    GenomeLoc before = new GenomeLoc(g.getContigIndex(), g.getStart(), e.getStart() - 1);
+                    GenomeLoc before = GenomeLocParser.createGenomeLoc(g.getContigIndex(), g.getStart(), e.getStart() - 1);
-                    GenomeLoc after = new GenomeLoc(g.getContigIndex(), e.getStop() + 1, g.getStop());
+                    GenomeLoc after = GenomeLocParser.createGenomeLoc(g.getContigIndex(), e.getStop() + 1, g.getStop());
                     int index = mArray.indexOf(g);
                     if (after.getStop() - after.getStart() > 0) {
                         mArray.add(index, after);
@@ -207,9 +207,9 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
                      */
 
                     if (e.getStart() < g.getStart()) {
-                        l = new GenomeLoc(g.getContigIndex(), e.getStop() + 1, g.getStop());
+                        l = GenomeLocParser.createGenomeLoc(g.getContigIndex(), e.getStop() + 1, g.getStop());
                     } else {
-                        l = new GenomeLoc(g.getContigIndex(), g.getStart(), e.getStart() - 1);
+                        l = GenomeLocParser.createGenomeLoc(g.getContigIndex(), g.getStart(), e.getStart() - 1);
                     }
                     // replace g with the new region
                     mArray.set(mArray.indexOf(g), l);
@@ -230,7 +230,7 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
     public static GenomeLocSortedSet createSetFromSequenceDictionary(SAMSequenceDictionary dict) {
         GenomeLocSortedSet returnSortedSet = new GenomeLocSortedSet();
         for (SAMSequenceRecord record : dict.getSequences()) {
-            returnSortedSet.add(new GenomeLoc(record.getSequenceIndex(), 1, record.getSequenceLength()));
+            returnSortedSet.add(GenomeLocParser.createGenomeLoc(record.getSequenceIndex(), 1, record.getSequenceLength()));
         }
         return returnSortedSet;
     }
@@ -258,7 +258,7 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
         GenomeLocSortedSet ret = new GenomeLocSortedSet();
         for (GenomeLoc loc : this.mArray) {
             // ensure a deep copy
-            ret.mArray.add(new GenomeLoc(loc.getContigIndex(), loc.getStart(), loc.getStop()));
+            ret.mArray.add(GenomeLocParser.createGenomeLoc(loc.getContigIndex(), loc.getStart(), loc.getStop()));
         }
         return ret;
     }

java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java

@@ -7,8 +7,6 @@ import net.sf.samtools.util.CloseableIterator;
 import java.io.InputStream;
 import java.io.ByteArrayInputStream;
 import java.io.UnsupportedEncodingException;
-import java.io.File;
-import java.util.Collections;
 import java.util.List;
 import java.util.Arrays;
 import java.util.Iterator;
@@ -16,8 +14,7 @@ import java.util.ArrayList;
 
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.gatk.iterators.NullSAMIterator;
+import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.gatk.Reads;
 /**
  * User: hanna
  * Date: Jun 11, 2009
@@ -54,11 +51,11 @@ public class ArtificialSAMFileReader extends SAMFileReader {
      */
     @Override
     public CloseableIterator<SAMRecord> query(final String sequence, final int start, final int end, final boolean contained) {
-        GenomeLoc region = new GenomeLoc(sequence, start, end);
+        GenomeLoc region = GenomeLocParser.createGenomeLoc(sequence, start, end);
         List<SAMRecord> coveredSubset = new ArrayList<SAMRecord>();
 
         for( SAMRecord read: reads ) {
-            GenomeLoc readPosition = new GenomeLoc(read);
+            GenomeLoc readPosition = GenomeLocParser.createGenomeLoc(read);
             if( contained && region.containsP(readPosition) ) coveredSubset.add(read);
             else if( !contained && readPosition.overlapsP(region) ) coveredSubset.add(read);
         }

java/test/org/broadinstitute/sting/gatk/datasources/providers/AllLocusViewTest.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.providers;
 
 import org.junit.Assert;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.LocusContext;
 import net.sf.samtools.SAMRecord;
 
@@ -40,13 +41,13 @@ public class AllLocusViewTest extends LocusViewTemplate {
         AllLocusView allLocusView = (AllLocusView)view;
 
         for( long i = bounds.getStart(); i <= bounds.getStop(); i++ ) {
-            GenomeLoc site = new GenomeLoc("chr1",i);
+            GenomeLoc site = GenomeLocParser.createGenomeLoc("chr1",i);
             LocusContext locusContext = allLocusView.next();
             Assert.assertEquals("Locus context location is incorrect", site, locusContext.getLocation() );
             int expectedReadsAtSite = 0;
 
             for( SAMRecord read: reads ) {
-                if(new GenomeLoc(read).containsP(locusContext.getLocation())) {
+                if(GenomeLocParser.createGenomeLoc(read).containsP(locusContext.getLocation())) {
                     Assert.assertTrue("Target locus context does not contain reads", locusContext.getReads().contains(read) );
                     expectedReadsAtSite++;
                 }

java/test/org/broadinstitute/sting/gatk/datasources/providers/CoveredLocusViewTest.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.providers;
 
 import org.junit.Assert;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.LocusContext;
 import net.sf.samtools.SAMRecord;
 
@@ -43,11 +44,11 @@ public class CoveredLocusViewTest extends LocusViewTemplate {
         CoveredLocusView coveredLocusView = (CoveredLocusView)view;
 
         for( long i = bounds.getStart(); i <= bounds.getStop(); i++ ) {
-            GenomeLoc site = new GenomeLoc("chr1",i);
+            GenomeLoc site = GenomeLocParser.createGenomeLoc("chr1",i);
 
             int expectedReadsAtSite = 0;
             for( SAMRecord read: reads ) {
-                if( new GenomeLoc(read).containsP(site) )
+                if( GenomeLocParser.createGenomeLoc(read).containsP(site) )
                     expectedReadsAtSite++;
             }
 
@@ -61,7 +62,7 @@ public class CoveredLocusViewTest extends LocusViewTemplate {
             Assert.assertEquals("Found wrong number of reads at site", expectedReadsAtSite, locusContext.getReads().size());
 
             for( SAMRecord read: reads ) {
-                if(new GenomeLoc(read).containsP(locusContext.getLocation()))
+                if(GenomeLocParser.createGenomeLoc(read).containsP(locusContext.getLocation()))
                     Assert.assertTrue("Target locus context does not contain reads", locusContext.getReads().contains(read) );
             }
         }

java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceViewTest.java

@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.datasources.providers;
 import org.junit.Test;
 import org.junit.Assert;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.shards.LocusShard;
 import org.broadinstitute.sting.gatk.iterators.GenomeLocusIterator;
@@ -32,7 +33,7 @@ public class LocusReferenceViewTest extends ReferenceViewTemplate {
      */
     @Test(expected=InvalidPositionException.class)
     public void testSingleBPFailure() {
-        Shard shard = new LocusShard( new GenomeLoc(0,1,50) );
+        Shard shard = new LocusShard( GenomeLocParser.createGenomeLoc(0,1,50) );
 
         ShardDataProvider dataProvider = new ShardDataProvider(shard,null,sequenceFile,null);
         LocusReferenceView view = new LocusReferenceView(dataProvider);
@@ -45,12 +46,12 @@ public class LocusReferenceViewTest extends ReferenceViewTemplate {
      */
     @Test(expected=InvalidPositionException.class)
     public void testBoundsFailure() {
-        Shard shard = new LocusShard( new GenomeLoc(0,1,50) );
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc(0,1,50) );
 
         ShardDataProvider dataProvider = new ShardDataProvider(shard,null,sequenceFile,null);
         LocusReferenceView view = new LocusReferenceView(dataProvider);
 
-        view.getReferenceBase(new GenomeLoc(0,51));
+        view.getReferenceBase(GenomeLocParser.createGenomeLoc(0,51));
     }
 
 

java/test/org/broadinstitute/sting/gatk/datasources/providers/LocusViewTemplate.java

@@ -1,31 +1,21 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
+import net.sf.picard.reference.ReferenceSequence;
+import net.sf.picard.reference.ReferenceSequenceFile;
+import net.sf.samtools.*;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.gatk.Reads;
+import org.broadinstitute.sting.gatk.datasources.shards.LocusShard;
+import org.broadinstitute.sting.gatk.datasources.shards.Shard;
+import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.junit.BeforeClass;
 import org.junit.Test;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.gatk.datasources.shards.Shard;
-import org.broadinstitute.sting.gatk.datasources.shards.LocusShard;
-import org.broadinstitute.sting.gatk.Reads;
 
-import java.io.FileNotFoundException;
 import java.io.File;
-import java.util.Collections;
+import java.io.FileNotFoundException;
-import java.util.List;
+import java.util.*;
-import java.util.Iterator;
-import java.util.ArrayList;
-import java.util.Arrays;
-
-import net.sf.picard.reference.ReferenceSequenceFile;
-import net.sf.picard.reference.ReferenceSequence;
-import net.sf.samtools.SAMSequenceDictionary;
-import net.sf.samtools.SAMSequenceRecord;
-import net.sf.samtools.SAMRecord;
-import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.Cigar;
-import net.sf.samtools.CigarElement;
-import net.sf.samtools.CigarOperator;
 /**
  * User: hanna
  * Date: May 13, 2009
@@ -49,14 +39,14 @@ public abstract class LocusViewTemplate extends BaseTest {
     @BeforeClass
     public static void setupGenomeLoc() throws FileNotFoundException {
         sequenceSourceFile = fakeReferenceSequenceFile();
-        GenomeLoc.setupRefContigOrdering(sequenceSourceFile);
+        GenomeLocParser.setupRefContigOrdering(sequenceSourceFile);
     }
 
     @Test
     public void emptyLocusContextTest() {
         SAMRecordIterator iterator = new SAMRecordIterator();
 
-        GenomeLoc shardBounds = new GenomeLoc("chr1",1,5);
+        GenomeLoc shardBounds = GenomeLocParser.createGenomeLoc("chr1",1,5);
         Shard shard = new LocusShard(shardBounds);
         ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
 
@@ -70,7 +60,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read = buildSAMRecord("chr1",1,5);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
-        GenomeLoc shardBounds = new GenomeLoc("chr1",1,5);
+        GenomeLoc shardBounds = GenomeLocParser.createGenomeLoc("chr1",1,5);
         Shard shard = new LocusShard(shardBounds);
         ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
 
@@ -84,7 +74,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read = buildSAMRecord("chr1",1,5);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
-        Shard shard = new LocusShard(new GenomeLoc("chr1",1,10));
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
         ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
         LocusView view = createView( dataProvider );
 
@@ -96,7 +86,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read = buildSAMRecord("chr1",6,10);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
-        Shard shard = new LocusShard(new GenomeLoc("chr1",1,10));
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
         ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
         LocusView view = createView( dataProvider );
 
@@ -108,7 +98,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read = buildSAMRecord("chr1",3,7);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
-        Shard shard = new LocusShard(new GenomeLoc("chr1",1,10));
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
         ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
         LocusView view = createView( dataProvider );
 
@@ -120,7 +110,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read = buildSAMRecord("chr1",1,10);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
-        Shard shard = new LocusShard(new GenomeLoc("chr1",6,15));
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",6,15));
         ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
         LocusView view = createView( dataProvider );
 
@@ -132,7 +122,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read = buildSAMRecord("chr1",6,15);
         SAMRecordIterator iterator = new SAMRecordIterator(read);
 
-        Shard shard = new LocusShard(new GenomeLoc("chr1",1,10));
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
         ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
         LocusView view = createView( dataProvider );
 
@@ -145,7 +135,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read2 = buildSAMRecord("chr1",6,10);
         SAMRecordIterator iterator = new SAMRecordIterator(read1,read2);
 
-        Shard shard = new LocusShard(new GenomeLoc("chr1",1,10));
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
         ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
         LocusView view = createView( dataProvider );
 
@@ -162,7 +152,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read4 = buildSAMRecord("chr1",6,10);
         SAMRecordIterator iterator = new SAMRecordIterator(read1,read2,read3,read4);
 
-        Shard shard = new LocusShard(new GenomeLoc("chr1",1,10));
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
         ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
         LocusView view = createView( dataProvider );
 
@@ -179,7 +169,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read4 = buildSAMRecord("chr1",5,9);
         SAMRecordIterator iterator = new SAMRecordIterator(read1,read2,read3,read4);
 
-        Shard shard = new LocusShard(new GenomeLoc("chr1",1,10));
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
         ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
         LocusView view = createView( dataProvider );
 
@@ -198,7 +188,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecord read6 = buildSAMRecord("chr1",6,10);
         SAMRecordIterator iterator = new SAMRecordIterator(read1,read2,read3,read4,read5,read6);
 
-        Shard shard = new LocusShard(new GenomeLoc("chr1",1,10));
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",1,10));
         ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
         LocusView view = createView( dataProvider );
 
@@ -224,7 +214,7 @@ public abstract class LocusViewTemplate extends BaseTest {
         SAMRecordIterator iterator = new SAMRecordIterator(read01,read02,read03,read04,read05,read06,
                                                            read07,read08,read09,read10,read11,read12);
 
-        Shard shard = new LocusShard(new GenomeLoc("chr1",6,15));
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chr1",6,15));
         ShardDataProvider dataProvider = new ShardDataProvider( shard, iterator );
         LocusView view = createView( dataProvider );
 

java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceOrderedViewTest.java

@@ -4,7 +4,7 @@ import org.junit.Test;
 import org.junit.BeforeClass;
 import org.junit.Assert;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.TabularROD;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -44,7 +44,7 @@ public class ReferenceOrderedViewTest extends BaseTest {
     public static void init() throws FileNotFoundException {
         // sequence
         seq = new IndexedFastaSequenceFile(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
-        GenomeLoc.setupRefContigOrdering(seq);
+        GenomeLocParser.setupRefContigOrdering(seq);
     }
 
     /**
@@ -52,11 +52,11 @@ public class ReferenceOrderedViewTest extends BaseTest {
      */
     @Test
     public void testNoBindings() {
-        Shard shard = new LocusShard(new GenomeLoc("chrM",1,30));
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chrM",1,30));
         ShardDataProvider provider = new ShardDataProvider(shard, null, seq, Collections.<ReferenceOrderedDataSource>emptyList());
         ReferenceOrderedView view = new ReferenceOrderedView( provider );
 
-        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(new GenomeLoc("chrM",10));
+        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(GenomeLocParser.createGenomeLoc("chrM",10));
         Assert.assertNull("The tracker should not have produced any data", tracker.lookup("tableTest",null));
     }
 
@@ -69,12 +69,12 @@ public class ReferenceOrderedViewTest extends BaseTest {
         ReferenceOrderedData rod = new ReferenceOrderedData("tableTest", file, TabularROD.class);
         ReferenceOrderedDataSource dataSource = new ReferenceOrderedDataSource(rod);
 
-        Shard shard = new LocusShard(new GenomeLoc("chrM",1,30));
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chrM",1,30));
 
         ShardDataProvider provider = new ShardDataProvider(shard, null, seq, Collections.singletonList(dataSource));
         ReferenceOrderedView view = new ReferenceOrderedView( provider );
 
-        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(new GenomeLoc("chrM",20));
+        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(GenomeLocParser.createGenomeLoc("chrM",20));
         TabularROD datum = (TabularROD)tracker.lookup("tableTest",null);
 
         Assert.assertEquals("datum parameter for COL1 is incorrect", "C", datum.get("COL1"));
@@ -95,12 +95,12 @@ public class ReferenceOrderedViewTest extends BaseTest {
         ReferenceOrderedDataSource dataSource2 = new ReferenceOrderedDataSource(rod2);
 
 
-        Shard shard = new LocusShard(new GenomeLoc("chrM",1,30));
+        Shard shard = new LocusShard(GenomeLocParser.createGenomeLoc("chrM",1,30));
 
         ShardDataProvider provider = new ShardDataProvider(shard, null, seq, Arrays.asList(dataSource1,dataSource2));
         ReferenceOrderedView view = new ReferenceOrderedView( provider );
 
-        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(new GenomeLoc("chrM",20));
+        RefMetaDataTracker tracker = view.getReferenceOrderedDataAtLocus(GenomeLocParser.createGenomeLoc("chrM",20));
         TabularROD datum1 = (TabularROD)tracker.lookup("tableTest1",null);
 
         Assert.assertEquals("datum1 parameter for COL1 is incorrect", "C", datum1.get("COL1"));

java/test/org/broadinstitute/sting/gatk/datasources/providers/ReferenceViewTemplate.java

@@ -1,15 +1,15 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
-import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
+import net.sf.samtools.SAMSequenceRecord;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.junit.BeforeClass;
 import org.junit.Test;
 
-import java.io.FileNotFoundException;
 import java.io.File;
-
+import java.io.FileNotFoundException;
-import net.sf.samtools.SAMSequenceRecord;
 /**
  * User: hanna
  * Date: May 27, 2009
@@ -43,7 +43,7 @@ public abstract class ReferenceViewTemplate extends BaseTest {
     @BeforeClass
     public static void initialize() throws FileNotFoundException {
         sequenceFile = new IndexedFastaSequenceFile( new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta") );
-        GenomeLoc.setupRefContigOrdering(sequenceFile);
+        GenomeLocParser.setupRefContigOrdering(sequenceFile);
     }
 
     /**
@@ -51,7 +51,7 @@ public abstract class ReferenceViewTemplate extends BaseTest {
      */
     @Test
     public void testReferenceStart() {
-        validateLocation( new GenomeLoc(0,1,25) );
+        validateLocation( GenomeLocParser.createGenomeLoc(0,1,25) );
     }
 
     /**
@@ -63,7 +63,7 @@ public abstract class ReferenceViewTemplate extends BaseTest {
         SAMSequenceRecord selectedContig = sequenceFile.getSequenceDictionary().getSequences().get(sequenceFile.getSequenceDictionary().getSequences().size()-1);
         final long contigStart = selectedContig.getSequenceLength() - 24;
         final long contigStop = selectedContig.getSequenceLength();
-        validateLocation( new GenomeLoc(selectedContig.getSequenceIndex(),contigStart,contigStop) );
+        validateLocation( GenomeLocParser.createGenomeLoc(selectedContig.getSequenceIndex(),contigStart,contigStop) );
     }
 
     /**
@@ -74,7 +74,7 @@ public abstract class ReferenceViewTemplate extends BaseTest {
         // Test the last 25 bases of the first contig.
         int contigPosition = sequenceFile.getSequenceDictionary().getSequences().size()/2;
         SAMSequenceRecord selectedContig = sequenceFile.getSequenceDictionary().getSequences().get(contigPosition);
-        validateLocation( new GenomeLoc(selectedContig.getSequenceIndex(),1,25) );
+        validateLocation( GenomeLocParser.createGenomeLoc(selectedContig.getSequenceIndex(),1,25) );
     }
 
 
@@ -88,7 +88,7 @@ public abstract class ReferenceViewTemplate extends BaseTest {
         SAMSequenceRecord selectedContig = sequenceFile.getSequenceDictionary().getSequences().get(contigPosition);
         final long contigStart = selectedContig.getSequenceLength() - 24;
         final long contigStop = selectedContig.getSequenceLength();
-        validateLocation( new GenomeLoc(selectedContig.getSequenceIndex(),contigStart,contigStop) );
+        validateLocation( GenomeLocParser.createGenomeLoc(selectedContig.getSequenceIndex(),contigStart,contigStop) );
     }
 
     protected abstract void validateLocation( GenomeLoc loc );

java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardStrategyTest.java

@@ -7,6 +7,7 @@ import static org.junit.Assert.assertTrue;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.BaseTest;
 import net.sf.samtools.SAMFileHeader;
@@ -60,7 +61,7 @@ public class IntervalShardStrategyTest extends BaseTest {
 
     @Before
     public void setup() {
-        GenomeLoc.setupRefContigOrdering(header.getSequenceDictionary());
+        GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary());
         mSortedSet = new GenomeLocSortedSet();
     }
 
@@ -71,7 +72,7 @@ public class IntervalShardStrategyTest extends BaseTest {
 
     @Test
     public void testSingleChromosomeFunctionality() {
-        GenomeLoc loc = new GenomeLoc(1, 1, 1000);
+        GenomeLoc loc = GenomeLocParser.createGenomeLoc(1, 1, 1000);
         mSortedSet.add(loc);
         IntervalShardStrategy strat = new IntervalShardStrategy(100, mSortedSet);
         int counter = 0;
@@ -87,7 +88,7 @@ public class IntervalShardStrategyTest extends BaseTest {
     @Test
     public void testMultipleChromosomeFunctionality() {
         for (int x = 0; x < 5; x++) {
-            GenomeLoc loc = new GenomeLoc(x, 1, 1000);
+            GenomeLoc loc = GenomeLocParser.createGenomeLoc(x, 1, 1000);
             mSortedSet.add(loc);
         }
         IntervalShardStrategy strat = new IntervalShardStrategy(100, mSortedSet);
@@ -104,7 +105,7 @@ public class IntervalShardStrategyTest extends BaseTest {
     @Test
     public void testOddSizeShardFunctionality() {
         for (int x = 0; x < 5; x++) {
-            GenomeLoc loc = new GenomeLoc(x, 1, 1000);
+            GenomeLoc loc = GenomeLocParser.createGenomeLoc(x, 1, 1000);
             mSortedSet.add(loc);
         }
         IntervalShardStrategy strat = new IntervalShardStrategy(789, mSortedSet);
@@ -122,7 +123,7 @@ public class IntervalShardStrategyTest extends BaseTest {
     @Test
     public void testInfiniteShardSize() {
         for (int x = 0; x < 5; x++) {
-            GenomeLoc loc = new GenomeLoc(x, 1, 1000);
+            GenomeLoc loc = GenomeLocParser.createGenomeLoc(x, 1, 1000);
             mSortedSet.add(loc);
         }
         IntervalShardStrategy strat = new IntervalShardStrategy(Long.MAX_VALUE, mSortedSet);
@@ -137,7 +138,7 @@ public class IntervalShardStrategyTest extends BaseTest {
 
     @Test(expected = UnsupportedOperationException.class)
     public void testRemove() {
-        GenomeLoc loc = new GenomeLoc(1, 1, 1000);
+        GenomeLoc loc = GenomeLocParser.createGenomeLoc(1, 1, 1000);
         mSortedSet.add(loc);
         IntervalShardStrategy strat = new IntervalShardStrategy(100, mSortedSet);
         strat.remove();

java/test/org/broadinstitute/sting/gatk/datasources/shards/IntervalShardTest.java

@@ -2,6 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.shards;
 
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.junit.Before;
 import org.junit.Test;
@@ -51,20 +52,20 @@ public class IntervalShardTest extends BaseTest {
 
     @Before
     public void setup() {
-        GenomeLoc.setupRefContigOrdering(header.getSequenceDictionary());
+        GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary());
     }
 
 
     @Test
     public void simpleReturn() {
-        GenomeLoc loc = new GenomeLoc(1, 1, 100);
+        GenomeLoc loc = GenomeLocParser.createGenomeLoc(1, 1, 100);
         intervalShard = new IntervalShard(loc);
         assertTrue(intervalShard.getGenomeLoc().equals(loc));
     }
 
     @Test
     public void ensureNotReference() {
-        GenomeLoc loc = new GenomeLoc(1, 1, 100);
+        GenomeLoc loc = GenomeLocParser.createGenomeLoc(1, 1, 100);
         intervalShard = new IntervalShard(loc);
         assertTrue(intervalShard.getGenomeLoc() != loc && intervalShard.getGenomeLoc().equals(loc));
     }

java/test/org/broadinstitute/sting/gatk/datasources/shards/LinearLocusShardStrategyTest.java

@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
-import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.BaseTest;
 import org.junit.Before;
@@ -52,7 +52,7 @@ public class LinearLocusShardStrategyTest extends BaseTest {
 
     @Before
     public void setup() {
-        GenomeLoc.setupRefContigOrdering(header.getSequenceDictionary());
+        GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary());
     }
 
     @Test

java/test/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactoryTest.java

@@ -6,6 +6,7 @@ import net.sf.samtools.SAMFileHeader;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.junit.*;
 import static org.junit.Assert.assertTrue;
@@ -42,7 +43,7 @@ public class ShardStrategyFactoryTest extends BaseTest {
 
     @Before
     public void setup() {
-        GenomeLoc.setupRefContigOrdering(header.getSequenceDictionary());
+        GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary());
         set = new GenomeLocSortedSet();
     }
 
@@ -54,7 +55,7 @@ public class ShardStrategyFactoryTest extends BaseTest {
 
     @Test
     public void testReadInterval() {
-        GenomeLoc l = new GenomeLoc(0,1,100);
+        GenomeLoc l = GenomeLocParser.createGenomeLoc(0,1,100);
         set.add(l);
         ShardStrategy st = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.READS,header.getSequenceDictionary(),100,set);
         assertTrue(st instanceof IntervalShardStrategy);
@@ -74,7 +75,7 @@ public class ShardStrategyFactoryTest extends BaseTest {
 
     @Test
     public void testExpInterval() {
-        GenomeLoc l = new GenomeLoc(0,1,100);
+        GenomeLoc l = GenomeLocParser.createGenomeLoc(0,1,100);
         set.add(l);
         ShardStrategy st = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.EXPONENTIAL,header.getSequenceDictionary(),100,set);
         assertTrue(st instanceof ExpGrowthLocusShardStrategy);
@@ -82,7 +83,7 @@ public class ShardStrategyFactoryTest extends BaseTest {
 
     @Test
     public void testLinearInterval() {
-        GenomeLoc l = new GenomeLoc(0,1,100);
+        GenomeLoc l = GenomeLocParser.createGenomeLoc(0,1,100);
         set.add(l);
         ShardStrategy st = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.LINEAR,header.getSequenceDictionary(),100,set);
         assertTrue(st instanceof LinearLocusShardStrategy);

java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataPoolTest.java

@@ -8,6 +8,7 @@ import static org.junit.Assert.assertTrue;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.refdata.TabularROD;
@@ -38,13 +39,13 @@ public class ReferenceOrderedDataPoolTest extends BaseTest {
 
     private ReferenceOrderedData<? extends ReferenceOrderedDatum> rod = null;
 
-    private final GenomeLoc testSite1 = new GenomeLoc("chrM",10);
+    private final GenomeLoc testSite1 = GenomeLocParser.createGenomeLoc("chrM",10);
-    private final GenomeLoc testSite2 = new GenomeLoc("chrM",20);
+    private final GenomeLoc testSite2 = GenomeLocParser.createGenomeLoc("chrM",20);
-    private final GenomeLoc testSite3 = new GenomeLoc("chrM",30);
+    private final GenomeLoc testSite3 = GenomeLocParser.createGenomeLoc("chrM",30);
 
     @BeforeClass
     public static void init() throws FileNotFoundException {
-        GenomeLoc.setupRefContigOrdering(new IndexedFastaSequenceFile(sequenceFile));
+        GenomeLocParser.setupRefContigOrdering(new IndexedFastaSequenceFile(sequenceFile));
         TabularROD.setDelimiter(TabularROD.DEFAULT_DELIMITER, TabularROD.DEFAULT_DELIMITER_REGEX);
     }
 

java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMBAMDataSourceTest.java

@@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy;
 import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategyFactory;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
 import org.broadinstitute.sting.gatk.Reads;
-import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 import org.junit.After;
 import org.junit.Before;
@@ -60,7 +60,7 @@ public class SAMBAMDataSourceTest extends BaseTest {
 
         // sequence
         seq = new FastaSequenceFile2(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
-        GenomeLoc.setupRefContigOrdering(seq.getSequenceDictionary());
+        GenomeLocParser.setupRefContigOrdering(seq.getSequenceDictionary());
     }
 
     /**

java/test/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMByReadsTest.java

@@ -10,6 +10,7 @@ import org.broadinstitute.sting.gatk.iterators.BoundedReadIterator;
 import org.broadinstitute.sting.gatk.iterators.*;
 import org.broadinstitute.sting.gatk.Reads;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMQueryIterator;
 import static org.junit.Assert.assertEquals;
@@ -76,7 +77,7 @@ public class SAMByReadsTest extends BaseTest {
     @Test
     public void testToUnmappedReads() {
         ArtificialResourcePool gen = new ArtificialResourcePool(1,10,100,1000);
-        GenomeLoc.setupRefContigOrdering(gen.getHeader().getSequenceDictionary());
+        GenomeLocParser.setupRefContigOrdering(gen.getHeader().getSequenceDictionary());
         try {
             int unmappedReadsSeen = 0;
             int iterations = 0;
@@ -109,7 +110,7 @@ public class SAMByReadsTest extends BaseTest {
     @Test
     public void testShardingOfReadsSize14() {
         ArtificialResourcePool gen = new ArtificialResourcePool(1,10,100,1000);
-        GenomeLoc.setupRefContigOrdering(gen.getHeader().getSequenceDictionary());
+        GenomeLocParser.setupRefContigOrdering(gen.getHeader().getSequenceDictionary());
         targetReadCount = 14;
         try {
             int iterations = 0;
@@ -159,7 +160,7 @@ public class SAMByReadsTest extends BaseTest {
     @Test
     public void testShardingOfReadsSize25() {
         ArtificialResourcePool gen = new ArtificialResourcePool(1,10,100,1000);
-        GenomeLoc.setupRefContigOrdering(gen.getHeader().getSequenceDictionary());
+        GenomeLocParser.setupRefContigOrdering(gen.getHeader().getSequenceDictionary());
         targetReadCount = 25;
         try {
             int iterations = 0;

java/test/org/broadinstitute/sting/gatk/iterators/BoundedReadIteratorTest.java

@@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategyFactory;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SimpleDataSourceLoadException;
 import org.broadinstitute.sting.gatk.Reads;
-import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
@@ -73,7 +73,7 @@ public class BoundedReadIteratorTest extends BaseTest {
 
         // sequence
         seq = new FastaSequenceFile2(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
-        GenomeLoc.setupRefContigOrdering(seq.getSequenceDictionary());
+        GenomeLocParser.setupRefContigOrdering(seq.getSequenceDictionary());
     }
 
 

java/test/org/broadinstitute/sting/gatk/refdata/TabularRODTest.java

@@ -8,15 +8,13 @@ import org.junit.*;
 import static org.junit.Assert.assertTrue;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
-import org.broadinstitute.sting.utils.RefHanger;
+import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.io.File;
 import java.io.PrintStream;
 import java.io.FileOutputStream;
 import java.io.FileNotFoundException;
 import java.util.Arrays;
-import java.util.List;
 import java.util.ArrayList;
 
 /**
@@ -33,7 +31,7 @@ public class TabularRODTest extends BaseTest {
     public static void init() {
         // sequence
         seq = new FastaSequenceFile2(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
-        GenomeLoc.setupRefContigOrdering(seq);
+        GenomeLocParser.setupRefContigOrdering(seq);
     }
 
     @Before
@@ -50,7 +48,7 @@ public class TabularRODTest extends BaseTest {
         logger.warn("Executing test1");
         TabularROD one = (TabularROD)iter.next();
         assertTrue(one.size() == 4);
-        assertTrue(one.getLocation().equals(new GenomeLoc("chrM", 10)));
+        assertTrue(one.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 10)));
         assertTrue(one.get("COL1").equals("A"));
         assertTrue(one.get("COL2").equals("B"));        
         assertTrue(one.get("COL3").equals("C"));
@@ -62,7 +60,7 @@ public class TabularRODTest extends BaseTest {
         TabularROD one = (TabularROD)iter.next();
         TabularROD two = (TabularROD)iter.next();
         assertTrue(two.size() == 4);
-        assertTrue(two.getLocation().equals(new GenomeLoc("chrM", 20)));
+        assertTrue(two.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 20)));
         assertTrue(two.get("COL1").equals("C"));
         assertTrue(two.get("COL2").equals("D"));
         assertTrue(two.get("COL3").equals("E"));
@@ -75,7 +73,7 @@ public class TabularRODTest extends BaseTest {
         TabularROD two = (TabularROD)iter.next();
         TabularROD three = (TabularROD)iter.next();
         assertTrue(three.size() == 4);
-        assertTrue(three.getLocation().equals(new GenomeLoc("chrM", 30)));
+        assertTrue(three.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 30)));
         assertTrue(three.get("COL1").equals("F"));
         assertTrue(three.get("COL2").equals("G"));
         assertTrue(three.get("COL3").equals("H"));
@@ -93,9 +91,9 @@ public class TabularRODTest extends BaseTest {
     @Test
     public void testSeek() {
         logger.warn("Executing testSeek");
-        TabularROD two = (TabularROD)iter.seekForward(new GenomeLoc("chrM", 20));
+        TabularROD two = (TabularROD)iter.seekForward(GenomeLocParser.createGenomeLoc("chrM", 20));
         assertTrue(two.size() == 4);
-        assertTrue(two.getLocation().equals(new GenomeLoc("chrM", 20)));
+        assertTrue(two.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 20)));
         assertTrue(two.get("COL1").equals("C"));
         assertTrue(two.get("COL2").equals("D"));
         assertTrue(two.get("COL3").equals("E"));
@@ -118,7 +116,7 @@ public class TabularRODTest extends BaseTest {
         logger.warn("Executing testDelim1");
         TabularROD one2 = (TabularROD)iter_commas.next();
         assertTrue(one2.size() == 5);
-        assertTrue(one2.getLocation().equals(new GenomeLoc("chrM", 10)));
+        assertTrue(one2.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 10)));
         assertTrue(one2.get("COL1").equals("A"));
         assertTrue(one2.get("COL2").equals("B"));
         assertTrue(one2.get("COL3").equals("C"));
@@ -135,7 +133,7 @@ public class TabularRODTest extends BaseTest {
         logger.warn("Executing testDelim1");
         TabularROD one2 = (TabularROD)iter_commas.next();
         assertTrue(one2.size() == 5);
-        assertTrue(one2.getLocation().equals(new GenomeLoc("chrM", 10)));
+        assertTrue(one2.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 10)));
         assertTrue(one2.get("COL1").equals("A"));
         assertTrue(one2.get("COL2").equals("B"));
         assertTrue(one2.get("COL3").equals("C"));
@@ -148,7 +146,7 @@ public class TabularRODTest extends BaseTest {
         ArrayList<String> header = new ArrayList<String>(Arrays.asList("HEADER", "col1", "col2", "col3"));
         assertTrue(TabularROD.headerString(header).equals("HEADER\tcol1\tcol2\tcol3"));
         String rowData = String.format("%d %d %d", 1, 2, 3);
-        TabularROD row = new TabularROD("myName", header, new GenomeLoc("chrM", 1), rowData.split(" "));
+        TabularROD row = new TabularROD("myName", header, GenomeLocParser.createGenomeLoc("chrM", 1), rowData.split(" "));
         System.out.println(">>>>> " + row.toString());
         assertTrue(row.toString().equals("chrM:1\t1\t2\t3"));
     }
@@ -166,11 +164,11 @@ public class TabularRODTest extends BaseTest {
         out.println(TabularROD.headerString(header));
 
         String rowData = String.format("%d %d %d", 1, 2, 3);
-        TabularROD row = new TabularROD("myName", header, new GenomeLoc("chrM", 1), rowData.split(" "));
+        TabularROD row = new TabularROD("myName", header, GenomeLocParser.createGenomeLoc("chrM", 1), rowData.split(" "));
         out.println(row.toString());
 
         rowData = String.format("%d %d %d", 3, 4, 5);
-        row = new TabularROD("myName", header, new GenomeLoc("chrM", 2), rowData.split(" "));
+        row = new TabularROD("myName", header, GenomeLocParser.createGenomeLoc("chrM", 2), rowData.split(" "));
         out.println(row.toString());
 
         ReferenceOrderedData ROD_commas = new ReferenceOrderedData("tableTest", outputFile, TabularROD.class);
@@ -178,14 +176,14 @@ public class TabularRODTest extends BaseTest {
 
         TabularROD one = (TabularROD)iter_commas.next();
         assertTrue(one.size() == 4);
-        assertTrue(one.getLocation().equals(new GenomeLoc("chrM", 1)));
+        assertTrue(one.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 1)));
         assertTrue(one.get("col1").equals("1"));
         assertTrue(one.get("col2").equals("2"));
         assertTrue(one.get("col3").equals("3"));
 
         TabularROD two = (TabularROD)iter_commas.next();
         assertTrue(two.size() == 4);
-        assertTrue(two.getLocation().equals(new GenomeLoc("chrM", 2)));
+        assertTrue(two.getLocation().equals(GenomeLocParser.createGenomeLoc("chrM", 2)));
         assertTrue(two.get("col1").equals("3"));
         assertTrue(two.get("col2").equals("4"));
         assertTrue(two.get("col3").equals("5"));
@@ -195,14 +193,14 @@ public class TabularRODTest extends BaseTest {
     public void testBadHeader1() {
         logger.warn("Executing testBadHeader1");
         ArrayList<String> header = new ArrayList<String>();
-        TabularROD row = new TabularROD("myName", header, new GenomeLoc("chrM", 1));        
+        TabularROD row = new TabularROD("myName", header, GenomeLocParser.createGenomeLoc("chrM", 1));
     }
 
     @Test (expected=RuntimeException.class )
     public void testBadHeader2() {
         logger.warn("Executing testBadHeader2");
         ArrayList<String> header = new ArrayList<String>(Arrays.asList("col1", "col2", "col3"));
-        TabularROD row = new TabularROD("myName", header, new GenomeLoc("chrM", 1));
+        TabularROD row = new TabularROD("myName", header, GenomeLocParser.createGenomeLoc("chrM", 1));
     }
 
     @Test (expected=RuntimeException.class )
@@ -211,6 +209,6 @@ public class TabularRODTest extends BaseTest {
         ArrayList<String> header = new ArrayList<String>(Arrays.asList("HEADER", "col1", "col2", "col3"));
         assertTrue(TabularROD.headerString(header).equals("HEADER\tcol1\tcol2\tcol3"));
         String rowData = String.format("%d %d %d %d", 1, 2, 3, 4);
-        TabularROD row = new TabularROD("myName", header, new GenomeLoc("chrM", 1), rowData.split(" "));
+        TabularROD row = new TabularROD("myName", header, GenomeLocParser.createGenomeLoc("chrM", 1), rowData.split(" "));
     }
 }

java/test/org/broadinstitute/sting/gatk/traversals/TraverseReadsTest.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.traversals;
 
 import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.gatk.Reads;
 import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.shards.ShardStrategy;
@@ -10,8 +11,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedData;
 import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
 import org.broadinstitute.sting.gatk.walkers.CountReadsWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.Reads;
+import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
 import static org.junit.Assert.fail;
@@ -116,7 +116,7 @@ public class TraverseReadsTest extends BaseTest {
         catch (FileNotFoundException ex) {
             throw new RuntimeException("File not found opening fasta file; please do this check before MicroManaging", ex);
         }
-        GenomeLoc.setupRefContigOrdering(ref);
+        GenomeLocParser.setupRefContigOrdering(ref);
 
         ShardStrategy shardStrategy = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.READS,
                 ref.getSequenceDictionary(),
@@ -148,7 +148,7 @@ public class TraverseReadsTest extends BaseTest {
             fail("Count read walker should return an interger.");
         }
         if (((Integer) accumulator) != 9721) {
-            fail("there should be 9721 mapped reads in the index file");
+            fail("there should be 9721 mapped reads in the index file, there was " + ((Integer) accumulator) );
         }
     }
 
@@ -156,7 +156,6 @@ public class TraverseReadsTest extends BaseTest {
     /** Test out that we can shard the file and iterate over every read */
     @Test
     public void testUnmappedReadCount() {
-
         IndexedFastaSequenceFile ref = null;
         try {
             ref = new IndexedFastaSequenceFile(refFile);
@@ -164,7 +163,7 @@ public class TraverseReadsTest extends BaseTest {
         catch (FileNotFoundException ex) {
             throw new RuntimeException("File not found opening fasta file; please do this check before MicroManaging", ex);
         }
-        GenomeLoc.setupRefContigOrdering(ref);
+        GenomeLocParser.setupRefContigOrdering(ref);
 
         ShardStrategy shardStrategy = ShardStrategyFactory.shatter(ShardStrategyFactory.SHATTER_STRATEGY.READS,
                 ref.getSequenceDictionary(),
@@ -195,7 +194,7 @@ public class TraverseReadsTest extends BaseTest {
             fail("Count read walker should return an interger.");
         }
         if (((Integer) accumulator) != 10000) {
-            fail("there should be 10000 mapped reads in the index file");
+            fail("there should be 10000 mapped reads in the index file, there was " + ((Integer) accumulator));
         }
     }
 

java/test/org/broadinstitute/sting/playground/gatk/walkers/indels/CleanedReadInjectorTest.java

@@ -3,8 +3,8 @@ package org.broadinstitute.sting.playground.gatk.walkers.indels;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.OutputTracker;
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMFileReader;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMFileWriter;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
@@ -47,7 +47,7 @@ public class CleanedReadInjectorTest extends BaseTest {
     @BeforeClass
     public static void initialize() throws FileNotFoundException {
         sequenceFile = new IndexedFastaSequenceFile( new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta") );
-        GenomeLoc.setupRefContigOrdering(sequenceFile);
+        GenomeLocParser.setupRefContigOrdering(sequenceFile);
     }
 
     @Test

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

@@ -0,0 +1,126 @@
+package org.broadinstitute.sting.utils;
+
+import static junit.framework.Assert.assertTrue;
+import net.sf.samtools.SAMFileHeader;
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
+import static org.junit.Assert.assertEquals;
+import org.junit.Test;
+
+
+/**
+ * @author aaron
+ *         <p/>
+ *         Class GenomeLocParserTest
+ *         <p/>
+ *         Test out the functionality of the new genome loc parser
+ */
+public class GenomeLocParserTest extends BaseTest {
+
+    @Test(expected = StingException.class)
+    public void testUnsetupException() {
+        GenomeLocParser.createGenomeLoc(0, 0, 0);
+    }
+
+    @Test
+    public void testKnownContigOrder() {
+        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10);
+        // assert that it's false when the contig ordering is not setup
+        assertTrue(!GenomeLocParser.hasKnownContigOrdering());
+        GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary());
+        // assert that it's true when it is setup
+        assertTrue(GenomeLocParser.hasKnownContigOrdering());
+    }
+
+    @Test(expected = RuntimeException.class)
+    public void testGetContigIndex() {
+        assertEquals(-1, GenomeLocParser.getContigIndex("blah")); // should be in the reference
+    }
+
+    @Test
+    public void testGetContigIndexValid() {
+        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10);
+        assertEquals(0, GenomeLocParser.getContigIndex("chr1")); // should be in the reference
+    }
+
+    @Test
+    public void testGetContigInfoUnknownContig() {
+        assertEquals(null, GenomeLocParser.getContigInfo("blah")); // should be in the reference
+    }
+
+
+    @Test
+    public void testGetContigInfoKnownContig() {
+        SAMFileHeader header = ArtificialSAMUtils.createArtificialSamHeader(1, 1, 10);
+        assertEquals("chr1".compareTo(GenomeLocParser.getContigInfo("chr1").getSequenceName()), 0); // should be in the reference
+    }
+
+    @Test(expected = StingException.class)
+    public void testParseBadString() {
+        GenomeLocParser.parseGenomeLoc("Bad:0-1");
+    }
+
+    @Test
+    public void testParseGoodString() {
+        GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1-100");
+        assertEquals(loc.getContigIndex(), 0);
+        assertEquals(100, loc.getStop());
+        assertEquals(1, loc.getStart());
+    }
+
+    @Test(expected = RuntimeException.class)
+    public void testParseBadLocations() {
+        GenomeLocParser.parseGenomeLocs("chr1:1-1;badChr:1-0");
+    }
+
+    @Test
+    public void testParseGoodLocations() {
+        GenomeLocParser.parseGenomeLocs("chr1:1-1;chr1:5-9");
+    }
+
+    @Test(expected = RuntimeException.class)
+    public void testParseGoodLocationsTooManySemiColons() {
+        GenomeLocParser.parseGenomeLocs("chr1:1-1;;chr1:5-9;");
+    }
+
+    @Test
+    public void testCreateGenomeLoc1() {
+        GenomeLoc loc = GenomeLocParser.createGenomeLoc("chr1", 1, 100);
+        assertEquals(loc.getContigIndex(), 0);
+        assertEquals(100, loc.getStop());
+        assertEquals(1, loc.getStart());
+    }
+
+    @Test
+    public void testCreateGenomeLoc2() {
+        GenomeLoc loc = GenomeLocParser.createGenomeLoc(0, 1, 100);
+        assertEquals(loc.getContigIndex(), 0);
+        assertEquals(100, loc.getStop());
+        assertEquals(1, loc.getStart());
+    }
+
+    @Test
+    public void testCreateGenomeLoc3() {
+        GenomeLoc loc = GenomeLocParser.createGenomeLoc(0, 1);
+        assertEquals(loc.getContigIndex(), 0);
+        assertEquals(1, loc.getStop());
+        assertEquals(1, loc.getStart());
+    }
+
+    @Test
+    public void testCreateGenomeLoc4() {
+        GenomeLoc loc = GenomeLocParser.createGenomeLoc("chr1", 1);
+        assertEquals(loc.getContigIndex(), 0);
+        assertEquals(1, loc.getStop());
+        assertEquals(1, loc.getStart());
+    }
+
+    @Test
+    public void testCreateGenomeLoc5() {
+        GenomeLoc loc = GenomeLocParser.createGenomeLoc(0,1,100);
+        GenomeLoc copy = GenomeLocParser.createGenomeLoc(loc);
+        assertEquals(copy.getContigIndex(), 0);
+        assertEquals(100, copy.getStop());
+        assertEquals(1, copy .getStart());
+    }
+}

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

@@ -44,13 +44,13 @@ public class GenomeLocSortedSetTest extends BaseTest {
 
     @Before
     public void setup() {
-        GenomeLoc.setupRefContigOrdering(header.getSequenceDictionary());
+        GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary());
         mSortedSet = new GenomeLocSortedSet();
     }
 
     @Test
     public void testAdd() {
-        GenomeLoc g = new GenomeLoc(1, 0, 0);
+        GenomeLoc g = GenomeLocParser.createGenomeLoc(1, 0, 0);
         assertTrue(mSortedSet.size() == 0);
         mSortedSet.add(g);
         assertTrue(mSortedSet.size() == 1);
@@ -59,7 +59,7 @@ public class GenomeLocSortedSetTest extends BaseTest {
     @Test
     public void testRemove() {
         assertTrue(mSortedSet.size() == 0);
-        GenomeLoc g = new GenomeLoc(1, 0, 0);
+        GenomeLoc g = GenomeLocParser.createGenomeLoc(1, 0, 0);
         mSortedSet.add(g);
         assertTrue(mSortedSet.size() == 1);
         mSortedSet.remove(g);
@@ -69,9 +69,9 @@ public class GenomeLocSortedSetTest extends BaseTest {
     @Test
     public void addRegion() {
         assertTrue(mSortedSet.size() == 0);
-        GenomeLoc g = new GenomeLoc(1, 1, 50);
+        GenomeLoc g = GenomeLocParser.createGenomeLoc(1, 1, 50);
         mSortedSet.add(g);
-        GenomeLoc f = new GenomeLoc(1, 30, 80);
+        GenomeLoc f = GenomeLocParser.createGenomeLoc(1, 30, 80);
         mSortedSet.addRegion(f);
         assertTrue(mSortedSet.size() == 1);
         
@@ -81,7 +81,7 @@ public class GenomeLocSortedSetTest extends BaseTest {
     @Test(expected = IllegalArgumentException.class)
     public void testAddDupplicate() {
         assertTrue(mSortedSet.size() == 0);
-        GenomeLoc g = new GenomeLoc(1, 0, 0);
+        GenomeLoc g = GenomeLocParser.createGenomeLoc(1, 0, 0);
         mSortedSet.add(g);
         assertTrue(mSortedSet.size() == 1);
         mSortedSet.add(g);
@@ -89,8 +89,8 @@ public class GenomeLocSortedSetTest extends BaseTest {
 
     @Test
     public void mergingOverlappingBelow() {
-        GenomeLoc g = new GenomeLoc(1, 0, 50);
+        GenomeLoc g = GenomeLocParser.createGenomeLoc(1, 0, 50);
-        GenomeLoc e = new GenomeLoc(1, 49, 100);
+        GenomeLoc e = GenomeLocParser.createGenomeLoc(1, 49, 100);
         assertTrue(mSortedSet.size() == 0);
         mSortedSet.add(g);
         assertTrue(mSortedSet.size() == 1);
@@ -105,8 +105,8 @@ public class GenomeLocSortedSetTest extends BaseTest {
 
     @Test
     public void mergingOverlappingAbove() {
-        GenomeLoc e = new GenomeLoc(1, 0, 50);
+        GenomeLoc e = GenomeLocParser.createGenomeLoc(1, 0, 50);
-        GenomeLoc g = new GenomeLoc(1, 49, 100);
+        GenomeLoc g = GenomeLocParser.createGenomeLoc(1, 49, 100);
         assertTrue(mSortedSet.size() == 0);
         mSortedSet.add(g);
         assertTrue(mSortedSet.size() == 1);
@@ -121,13 +121,13 @@ public class GenomeLocSortedSetTest extends BaseTest {
 
     @Test
     public void deleteSubRegion() {
-        GenomeLoc e = new GenomeLoc(1, 0, 50);
+        GenomeLoc e = GenomeLocParser.createGenomeLoc(1, 0, 50);
-        GenomeLoc g = new GenomeLoc(1, 49, 100);
+        GenomeLoc g = GenomeLocParser.createGenomeLoc(1, 49, 100);
         mSortedSet.add(g);
         mSortedSet.addRegion(e);
 
         // now delete a region
-        GenomeLoc d = new GenomeLoc(1, 25, 75);
+        GenomeLoc d = GenomeLocParser.createGenomeLoc(1, 25, 75);
         mSortedSet.removeRegion(d);
         Iterator<GenomeLoc> iter = mSortedSet.iterator();
         GenomeLoc loc = iter.next();
@@ -143,20 +143,20 @@ public class GenomeLocSortedSetTest extends BaseTest {
 
     @Test
     public void deleteAllByRegion() {
-        GenomeLoc e = new GenomeLoc(1, 1, 100);
+        GenomeLoc e = GenomeLocParser.createGenomeLoc(1, 1, 100);
         mSortedSet.add(e);
         for (int x = 1; x < 101; x++) {
-            GenomeLoc del = new GenomeLoc(1,x,x);
+            GenomeLoc del = GenomeLocParser.createGenomeLoc(1,x,x);
             mSortedSet.removeRegion(del);
         }
         assertTrue(mSortedSet.isEmpty());
     }
     @Test
     public void deleteSomeByRegion() {
-        GenomeLoc e = new GenomeLoc(1, 1, 100);
+        GenomeLoc e = GenomeLocParser.createGenomeLoc(1, 1, 100);
         mSortedSet.add(e);
         for (int x = 1; x < 50; x++) {
-            GenomeLoc del = new GenomeLoc(1,x,x);
+            GenomeLoc del = GenomeLocParser.createGenomeLoc(1,x,x);
             mSortedSet.removeRegion(del);
         }
         assertTrue(!mSortedSet.isEmpty());
@@ -169,13 +169,13 @@ public class GenomeLocSortedSetTest extends BaseTest {
 
     @Test
     public void deleteSuperRegion() {
-        GenomeLoc e = new GenomeLoc(1, 10, 20);
+        GenomeLoc e = GenomeLocParser.createGenomeLoc(1, 10, 20);
-        GenomeLoc g = new GenomeLoc(1, 70, 100);
+        GenomeLoc g = GenomeLocParser.createGenomeLoc(1, 70, 100);
         mSortedSet.add(g);
         mSortedSet.addRegion(e);
         assertTrue(mSortedSet.size() == 2);
         // now delete a region
-        GenomeLoc d = new GenomeLoc(1, 15, 75);
+        GenomeLoc d = GenomeLocParser.createGenomeLoc(1, 15, 75);
         mSortedSet.removeRegion(d);
         Iterator<GenomeLoc> iter = mSortedSet.iterator();
         GenomeLoc loc = iter.next();

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

@@ -22,7 +22,7 @@ public class GenomeLocTest extends BaseTest {
     public static void init() {
         // sequence
         seq = new FastaSequenceFile2(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
-        GenomeLoc.setupRefContigOrdering(seq);
+        GenomeLocParser.setupRefContigOrdering(seq);
     }
 
     /**
@@ -32,10 +32,10 @@ public class GenomeLocTest extends BaseTest {
     public void testIsBetween() {
         logger.warn("Executing testIsBetween");
 
-        GenomeLoc locMiddle = new GenomeLoc("chr1", 3, 3);
+        GenomeLoc locMiddle = GenomeLocParser.createGenomeLoc("chr1", 3, 3);
 
-        GenomeLoc locLeft = new GenomeLoc("chr1", 1, 1);
+        GenomeLoc locLeft = GenomeLocParser.createGenomeLoc("chr1", 1, 1);
-        GenomeLoc locRight = new GenomeLoc("chr1", 5, 5);
+        GenomeLoc locRight = GenomeLocParser.createGenomeLoc("chr1", 5, 5);
 
         Assert.assertTrue(locMiddle.isBetween(locLeft, locRight));
         Assert.assertFalse(locLeft.isBetween(locMiddle, locRight));
@@ -45,15 +45,15 @@ public class GenomeLocTest extends BaseTest {
     @Test
     public void testContigIndex() {
         logger.warn("Executing testContigIndex");
-        GenomeLoc locOne = new GenomeLoc("chr1",1,1);
+        GenomeLoc locOne = GenomeLocParser.createGenomeLoc("chr1",1,1);
         Assert.assertEquals(locOne.getContigIndex(), 1);
         Assert.assertEquals(locOne.getContig(), "chr1");
 
-        GenomeLoc locX = new GenomeLoc("chrX",1,1);
+        GenomeLoc locX = GenomeLocParser.createGenomeLoc("chrX",1,1);
         Assert.assertEquals(locX.getContigIndex(), 23);
         Assert.assertEquals(locX.getContig(), "chrX");
 
-        GenomeLoc locNumber = new GenomeLoc(1,1,1);
+        GenomeLoc locNumber = GenomeLocParser.createGenomeLoc(1,1,1);
         Assert.assertEquals(locNumber.getContigIndex(), 1);
         Assert.assertEquals(locNumber.getContig(), "chr1");
         Assert.assertEquals(locOne.compareTo(locNumber), 0);
@@ -63,15 +63,15 @@ public class GenomeLocTest extends BaseTest {
     @Test
     public void testCompareTo() {
         logger.warn("Executing testCompareTo");
-        GenomeLoc twoOne = new GenomeLoc("chr2", 1);
+        GenomeLoc twoOne = GenomeLocParser.createGenomeLoc("chr2", 1);
-        GenomeLoc twoFive = new GenomeLoc("chr2", 5);
+        GenomeLoc twoFive = GenomeLocParser.createGenomeLoc("chr2", 5);
-        GenomeLoc twoOtherFive = new GenomeLoc("chr2", 5);
+        GenomeLoc twoOtherFive = GenomeLocParser.createGenomeLoc("chr2", 5);
         Assert.assertEquals(0, twoFive.compareTo(twoOtherFive));
 
         Assert.assertEquals(-1, twoOne.compareTo(twoFive));
         Assert.assertEquals(1, twoFive.compareTo(twoOne));
 
-        GenomeLoc oneOne = new GenomeLoc("chr1", 5);
+        GenomeLoc oneOne = GenomeLocParser.createGenomeLoc("chr1", 5);
         Assert.assertEquals(-1, oneOne.compareTo(twoOne));
         Assert.assertEquals(1, twoOne.compareTo(oneOne));
     }

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

@@ -4,11 +4,12 @@ package org.broadinstitute.sting.utils;
 
 // the imports for unit testing.
 
-import org.junit.*;
-import static org.junit.Assert.assertTrue;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.fasta.FastaSequenceFile2;
-import org.broadinstitute.sting.utils.RefHanger;
+import static org.junit.Assert.assertTrue;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
 
 import java.io.File;
 import java.util.Arrays;
@@ -69,7 +70,7 @@ public class RefHangerTest extends BaseTest {
     public static void init() {
         // sequence
         seq = new FastaSequenceFile2(new File(seqLocation + "/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"));
-        GenomeLoc.setupRefContigOrdering(seq);
+        GenomeLocParser.setupRefContigOrdering(seq);
 
         System.out.printf("Filled hanger is %n%s%n", makeFilledHanger());
     }
@@ -81,7 +82,7 @@ public class RefHangerTest extends BaseTest {
         l3 = Arrays.asList(6);
         l4 = Arrays.asList(7, 8);
         l5 = Arrays.asList(9, 10);
-        p1 = new GenomeLoc(0, 1, 1);
+        p1 = GenomeLocParser.createGenomeLoc(0, 1, 1);
         p2 = new GenomeLoc(p1).nextLoc();
         p3 = new GenomeLoc(p2).nextLoc();
         p4 = new GenomeLoc(p3).nextLoc();
@@ -94,7 +95,7 @@ public class RefHangerTest extends BaseTest {
 
     @Before
     public void setupHanger() {
-        startLoc = new GenomeLoc(0, 1, 1);  // chrM 1
+        startLoc = GenomeLocParser.createGenomeLoc(0, 1, 1);  // chrM 1
         emptyHanger = new RefHanger<Integer>();
         filledHanger = makeFilledHanger();
 
@@ -145,7 +146,7 @@ public class RefHangerTest extends BaseTest {
         assertTrue(filledHanger.hasLocation(p3));
         assertTrue(filledHanger.hasLocation(p4));
         assertTrue(filledHanger.hasLocation(p5));
-        assertTrue(! filledHanger.hasLocation(new GenomeLoc(0, 6, 6)));
+        assertTrue(! filledHanger.hasLocation(GenomeLocParser.createGenomeLoc(0, 6, 6)));
 
         assertTrue(filledHanger.getHanger(0) != null);
         assertTrue(filledHanger.getHanger(1) != null);