Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

public/java/src/org/broadinstitute/sting/utils/GenomeLocComparator.java

@@ -0,0 +1,56 @@
+package org.broadinstitute.sting.utils;
+
+import com.google.java.contract.Ensures;
+import com.google.java.contract.Requires;
+
+import java.util.Comparator;
+
+/**
+ *
+ * @author Mauricio Carneiro
+ * @since 9/28/11
+ */
+public class GenomeLocComparator implements Comparator<GenomeLoc> {
+    /**
+     * compares genomeLoc's contigs
+     *
+     * @param gl1 the genome loc to compare contigs
+     * @param gl2 the genome loc to compare contigs
+     * @return 0 if equal, -1 if gl2.contig is greater, 1 if gl1.contig is greater
+     */
+    @Requires("gl2 != null")
+    @Ensures("result == 0 || result == 1 || result == -1")
+    public final int compareContigs( GenomeLoc gl1, GenomeLoc gl2 ) {
+        if (gl1.contigIndex == gl2.contigIndex)
+            return 0;
+        else if (gl1.contigIndex > gl2.contigIndex)
+            return 1;
+        return -1;
+    }
+
+    @Requires("gl2 != null")
+    @Ensures("result == 0 || result == 1 || result == -1")
+    public int compare ( GenomeLoc gl1, GenomeLoc gl2 ) {
+        int result = 0;
+
+        if ( gl1 == gl2 ) {
+            result = 0;
+        }
+        else if(GenomeLoc.isUnmapped(gl1))
+            result = 1;
+        else if(GenomeLoc.isUnmapped(gl2))
+            result = -1;
+        else {
+            final int cmpContig = compareContigs(gl1, gl2);
+
+            if ( cmpContig != 0 ) {
+                result = cmpContig;
+            } else {
+                if ( gl1.getStart() < gl2.getStart() ) result = -1;
+                if ( gl1.getStart() > gl2.getStart() ) result = 1;
+            }
+        }
+
+        return result;
+    }
+}

public/java/src/org/broadinstitute/sting/utils/clipreads/ReadClipper.java

@@ -93,8 +93,9 @@ public class ReadClipper {
     public SAMRecord hardClipBothEndsByReferenceCoordinates(int left, int right) {
         if (left == right)
             return new SAMRecord(read.getHeader());
-        this.read = hardClipByReferenceCoordinates(right, -1);
+        SAMRecord leftTailRead = hardClipByReferenceCoordinates(right, -1);
-        return hardClipByReferenceCoordinates(-1, left);
+        ReadClipper clipper = new ReadClipper(leftTailRead);
+        return clipper.hardClipByReferenceCoordinatesLeftTail(left);
     }
 
     public SAMRecord hardClipLowQualEnds(byte lowQual) {

public/java/src/org/broadinstitute/sting/utils/sam/ReadUtils.java

@@ -893,6 +893,10 @@ public class ReadUtils {
                     // base before the deletion (see warning in function contracts)
                     else if (fallsInsideDeletion && !endsWithinCigar)
                         readBases += shift - 1;
+
+                    // If we reached our goal inside a deletion then we must backtrack to the last base before the deletion
+                    else if (fallsInsideDeletion && endsWithinCigar)
+                        readBases--;
                     }
             }