A fix for the 'rod blows up when it hits a GenomeLoc outside the reference' issu

e.  Really a stopgap; error handling in the RODs needs to be addressed in a more comprehensive way.  Right now, hasNext() isn't guaranteed to be correct.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@878 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -79,7 +79,7 @@ public class HapMapAlleleFrequenciesROD extends BasicReferenceOrderedDatum {
             varFreq = Double.parseDouble(parts[11]); // CEU_var_freq
             totalCounts = Integer.parseInt(parts[12]); // CEU_var
 
-            loc = new GenomeLoc(contig, start, stop);
+            loc = GenomeLoc.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/ReferenceOrderedData.java

@@ -14,6 +14,7 @@ import org.broadinstitute.sting.gatk.refdata.rodRefSeq;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.xReadLines;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.MalformedGenomeLocException;
 import org.apache.log4j.Logger;
 
 /**
@@ -263,11 +264,36 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
         }
 
         public ROD next() {
-            final String line = parser.next();
+            ROD n = null;
-            //System.out.printf("Line is %s%n", line);
+            boolean success = false;
-            String parts[] = line.split(fieldDelimiter);
+            boolean firstFailure = true;
-            ROD n = parseLine(parts);
+
-            return n != null ? n : next();
+            do {
+                final String line = parser.next();
+                //System.out.printf("Line is %s%n", line);
+                String parts[] = line.split(fieldDelimiter);
+                
+                try {
+                    n = parseLine(parts);
+                    // Two failure conditions:
+                    // 1) parseLine throws an exception.
+                    // 2) parseLine returns null.
+                    // 3) parseLine throws a RuntimeException.
+                    // TODO: Clean this up so that all errors are handled in one spot.
+                    success = (n != null);
+                }
+                catch( MalformedGenomeLocException ex ) {
+                    if( firstFailure ) {
+                        Utils.warnUser("Failed to parse contig on line '" + line + "'.  Skipping ahead to the next recognized GenomeLoc.");
+                        firstFailure = false;
+                    }
+                    if( !parser.hasNext() )
+                        Utils.warnUser("Unable to find more valid reference-ordered data.  Giving up.");
+                }
+
+            } while (!success && parser.hasNext());
+
+            return n;
         }
  
         public void remove() {
@@ -308,7 +334,8 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
         public boolean hasNext() { return it.hasNext(); }
         public ROD next() {
             ROD next = it.next();
-            position = next.getLocation().clone();
+            if( next != null )
+                position = next.getLocation().clone();
             return next; 
         }
 
@@ -336,6 +363,8 @@ public class ReferenceOrderedData<ROD extends ReferenceOrderedDatum> implements
             if ( DEBUG ) System.out.printf("  *** starting seek to %s %d%n", loc.getContig(), loc.getStart());
             while ( hasNext() ) {
                 ROD current = next();
+                if( current == null )
+                    continue;
                 //System.out.printf("    -> Seeking to %s %d AT %s %d%n", contigName, pos, current.getContig(), current.getStart());
                 int cmp = current.getLocation().compareTo(loc);
                 if ( cmp < 0 ) {

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

@@ -170,8 +170,8 @@ class SAMPileupRecord implements Genotype, GenotypeList, Pileup {
             if ( refBaseChar == '*' ) {
             	
                 parseIndels(parts[3]) ;
-                if ( varType == DELETION_VARIANT ) loc = new GenomeLoc(contig, start, start+eventLength-1);
+                if ( varType == DELETION_VARIANT ) loc = GenomeLoc.parseGenomeLoc(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 = 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 {
                 parseBasesAndQuals(parts[8], parts[9]);
@@ -180,8 +180,8 @@ class SAMPileupRecord implements Genotype, GenotypeList, Pileup {
                 
                 refBases = parts[2].toUpperCase();
                 eventLength = 1;
-                //loc = new GenomeLoc(contig, start, start+1);
+                //loc = GenomeLoc.parseGenomeLoc(contig, start, start+1);
-                loc = new GenomeLoc(contig, start, start);
+                loc = GenomeLoc.parseGenomeLoc(contig, start, start);
 
                 char ch = parts[3].charAt(0);
 

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

@@ -35,7 +35,7 @@ import org.apache.log4j.Logger;
  * 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, GenomeLoc.parseGenomeLoc("chrM", 1), rowData.split(" "));
  * assertTrue(row.toString().equals("chrM:1\t1\t2\t3"));
  */
 public class TabularROD extends BasicReferenceOrderedDatum implements Map<String, String> {

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

@@ -75,8 +75,8 @@ public class Transcript {
 			else throw new StingException("Expected strand symbol (+/-), found: "+fields[3]);
 			
 			String contig_name = fields[2];
-			transcript_interval = new GenomeLoc(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5]));
+			transcript_interval = GenomeLoc.parseGenomeLoc(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5]));
-			transcript_coding_interval = new GenomeLoc(contig_name, Integer.parseInt(fields[6])+1, Integer.parseInt(fields[7]));
+			transcript_coding_interval = GenomeLoc.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 +89,7 @@ public class Transcript {
 			exon_frames = new ArrayList<Integer>(eframes.length);
 			
 			for ( int i = 0 ; i < exon_starts.length  ; i++ ) {
-				exons.add(new GenomeLoc(contig_name, Integer.parseInt(exon_starts[i])+1, Integer.parseInt(exon_stops[i]) ) );
+				exons.add(GenomeLoc.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

@@ -7,6 +7,7 @@ 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.gatk.refdata.AllelicVariant;
 
 /**
@@ -161,7 +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 = new GenomeLoc(contig, start, stop);
+            loc = GenomeLoc.parseGenomeLoc(contig, start, stop);
 
             name = parts[4];
             refBases = parts[5];
@@ -177,8 +178,11 @@ public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVaria
             weight = Integer.parseInt(parts[17]);
             //System.out.printf("Parsed %s%n", toString());
             return true;
+        } catch( MalformedGenomeLocException ex ) {
+            // Just rethrow malformed genome locs; the ROD system itself will deal with these.
+            throw ex;
         } catch ( RuntimeException e ) {
-            System.out.printf("  Exception caught during parsing GFFLine %s%n", Utils.join(" <=> ", parts));
+            System.out.printf("  Exception caught during parsing DBSNP line %s%n", Utils.join(" <=> ", parts));
             throw e;
         }
     }

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

@@ -73,7 +73,7 @@ public class rodGFF extends BasicReferenceOrderedDatum {
     }
 
     public GenomeLoc getLocation() {
-        return new GenomeLoc(contig, start, stop);
+        return GenomeLoc.parseGenomeLoc(contig, start, stop);
     }
 
     public String getAttribute(final String key) {

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

@@ -21,7 +21,7 @@ public class rodRefSeq extends BasicReferenceOrderedDatum {
 	
 	public rodRefSeq(String name) {
 		super(name);
-//		location = new GenomeLoc(0,0,-1);
+//		location = GenomeLoc.parseGenomeLoc(0,0,-1);
 	}
 
 	/** Despite this constructor is public, it is meant primarily for the internal use; RefSeq iterator will
@@ -182,7 +182,7 @@ 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,new GenomeLoc(curr_contig_name,curr_position, curr_position),Collections.unmodifiableList(records));
+		rodRefSeq rod = new rodRefSeq(name,GenomeLoc.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/utils/GenomeLoc.java

@@ -87,7 +87,7 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
     public 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."); }
 
-        if (contigIndex < 0 || contigIndex >= contigInfo.size()) {
+        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);}
@@ -128,6 +128,19 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
         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 + " is not within installed 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);
@@ -184,7 +197,10 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
             stop = getContigInfo(contig).getSequenceLength();
         }
 
-        GenomeLoc loc = new GenomeLoc(contig, start, stop);
+        if( !isContigValid(contig) )
+            throw new MalformedGenomeLocException("Contig " + contig + " is not within installed 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;
@@ -583,4 +599,24 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable {
             }
         }
     }
+
+    /**
+     * 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/MalformedGenomeLocException.java

@@ -0,0 +1,37 @@
+package org.broadinstitute.sting.utils;
+/**
+ * User: hanna
+ * Date: Jun 2, 2009
+ * Time: 11:43:48 AM
+ * BROAD INSTITUTE SOFTWARE COPYRIGHT NOTICE AND AGREEMENT
+ * Software and documentation are copyright 2005 by the Broad Institute.
+ * All rights are reserved.
+ *
+ * Users acknowledge that this software is supplied without any warranty or support.
+ * The Broad Institute is not responsible for its use, misuse, or
+ * functionality.
+ */
+
+/**
+ * Indicates that something was wrong with in the parameters passed to create a GenomeLoc...
+ * bad sequence id out of bounds, etc.
+ */
+
+public class MalformedGenomeLocException extends StingException {
+    /**
+     * Create a new MalformedGenomeLocException with the given message.  Does not preserve the existing stack trace.
+     * @param message The message.
+     */
+    public MalformedGenomeLocException( String message ) {
+        super(message);
+    }
+
+    /**
+     * Create a new MalformedGenomeLocException with the given message and root cause.
+     * @param message The message.
+     * @param t The root cause.
+     */
+    public MalformedGenomeLocException( String message, Throwable t ) {
+        super(message,t);
+    }
+}