add a fix so that XL arguments won't cancel out -BTI arguments, fixed a bug for Ben where the ROD -> interval list conversion was throwing an exception, and some old code removal.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3174 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -184,7 +184,9 @@ public class GenomeAnalysisEngine {
             // if include argument isn't given, create new set of all possible intervals
             GenomeLocSortedSet includeSortedSet = (argCollection.intervals == null && argCollection.RODToInterval == null ?
                     GenomeLocSortedSet.createSetFromSequenceDictionary(this.referenceDataSource.getSequenceDictionary()) :
-                    loadIntervals(argCollection.intervals, argCollection.intervalMerging));
+                    loadIntervals(argCollection.intervals,
+                                  argCollection.intervalMerging,
+                                  GenomeLocParser.mergeIntervalLocations(checkRODToIntervalArgument(),argCollection.intervalMerging)));
 
             // if no exclude arguments, can return parseIntervalArguments directly
             if (argCollection.excludeIntervals == null)
@@ -192,7 +194,7 @@ public class GenomeAnalysisEngine {
 
             // otherwise there are exclude arguments => must merge include and exclude GenomeLocSortedSets
             else {
-                GenomeLocSortedSet excludeSortedSet = loadIntervals(argCollection.excludeIntervals, argCollection.intervalMerging);
+                GenomeLocSortedSet excludeSortedSet = loadIntervals(argCollection.excludeIntervals, argCollection.intervalMerging, null);
                 intervals = includeSortedSet.subtractRegions(excludeSortedSet);
 
                 // logging messages only printed when exclude (-XL) arguments are given
@@ -208,16 +210,16 @@ public class GenomeAnalysisEngine {
     }
 
     /**
-     * Loads the intervals relevant to
+     * Loads the intervals relevant to the current execution
      * @param argList String representation of arguments; might include 'all', filenames, intervals in samtools
      *                notation, or a combination of the
      * @param mergingRule Technique to use when merging interval data.
+     * @param additionalIntervals a list of additional intervals to add to the returned set.  Can be null.
      * @return A sorted, merged list of all intervals specified in this arg list.
      */
-    private GenomeLocSortedSet loadIntervals(List<String> argList, IntervalMergingRule mergingRule) {
+    private GenomeLocSortedSet loadIntervals(List<String> argList, IntervalMergingRule mergingRule, List<GenomeLoc> additionalIntervals) {
-        List<GenomeLoc> rawIntervals = new ArrayList<GenomeLoc>();    // running list of raw GenomeLocs
+        List<GenomeLoc> rawIntervals = (additionalIntervals == null) ? new ArrayList<GenomeLoc>() : additionalIntervals;  // running list of raw GenomeLocs
-        // TODO: Aaron, how do we discriminate between RODs that are for inclusion and RODs that are for exclusion?
+
-        rawIntervals.addAll(checkRODToIntervalArgument());            // add any RODs-to-intervals we have
         rawIntervals.addAll(IntervalUtils.parseIntervalArguments(argList));
 
         // redundant check => default no arguments is null, not empty list

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

@@ -317,43 +317,6 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
         return ret;
     }
 
-
-    public boolean addAllRegions(List<GenomeLoc> locations) {
-        this.mArray.addAll(locations);
-        Collections.sort(this.mArray);
-        this.mArray = GenomeLocSortedSet.mergeOverlappingLocations(this.mArray);
-        return true;
-    }
-
-/**
-     * 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: " + Utils.join(", ", 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;
-        }
-    }
-
     /**
      * convert this object to a list
      * @return the lists

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

@@ -217,31 +217,4 @@ public class GenomeLocSortedSetUnitTest extends BaseTest {
         }
         assertTrue(seqNumber == GenomeLocSortedSetUnitTest.NUMBER_OF_CHROMOSOMES);
     }
-
-    @Test
-    public void testAddAll() {
-        mSortedSet = GenomeLocSortedSet.createSetFromSequenceDictionary(this.header.getSequenceDictionary());
-        GenomeLocSortedSet set = GenomeLocSortedSet.createSetFromSequenceDictionary(this.header.getSequenceDictionary());
-        // we should have sequence
-        assertTrue(mSortedSet.size() == GenomeLocSortedSetUnitTest.NUMBER_OF_CHROMOSOMES);
-        mSortedSet.addAllRegions(set.toList());
-        assertTrue(mSortedSet.size() == GenomeLocSortedSetUnitTest.NUMBER_OF_CHROMOSOMES);                        
-    }
-
-    @Test
-    public void testAddAll2() {
-        mSortedSet = new GenomeLocSortedSet();
-        GenomeLocSortedSet mSortedSet2 = new GenomeLocSortedSet();
-        for (int x=0; x < 200; x = x + 2) {
-            mSortedSet.add(GenomeLocParser.createGenomeLoc(1,x));
-        }
-        assertEquals(100, mSortedSet.size());
-        for (int x=1; x < 201; x = x + 2) {
-            mSortedSet2.add(GenomeLocParser.createGenomeLoc(1,x));
-        }
-        assertEquals(100, mSortedSet2.size());
-        mSortedSet.addAllRegions(mSortedSet2.toList());
-        assertEquals(1, mSortedSet.size());
-    }
-
 }