Cleanup emergency fixes for out-of-bounds issues in reference retrieval. Fix spelling mistakes.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1173 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java

@@ -70,17 +70,12 @@ public class LocusReferenceView extends ReferenceView {
 
     /**
      * Allow the user to pull reference info from any arbitrary region of the reference.
-     * Assume the user has already performed all necessary bounds checking.
-     * TODO: This function is nearly identical to that in the ReadReferenceView.  Merge the common functionality.
      * @param genomeLoc The locus.
      * @return A list of the bases starting at the start of the locus (inclusive) and ending
      *         at the end of the locus (inclusive).
      */
     public char[] getReferenceBases( GenomeLoc genomeLoc ) {
-        SAMSequenceRecord sequenceInfo = reference.getSequenceDictionary().getSequence(genomeLoc.getContig());
+        return super.getReferenceBases(genomeLoc);
-        long stop = Math.min( genomeLoc.getStop(), sequenceInfo.getSequenceLength() );
-        ReferenceSequence subsequence = reference.getSubsequenceAt(genomeLoc.getContig(),genomeLoc.getStart(),stop);
-        return (StringUtil.bytesToString(subsequence.getBases()) + Utils.dupString('X', (int)(genomeLoc.getStop() - stop)) ).toCharArray();
     }
 
     /**

java/src/org/broadinstitute/sting/gatk/datasources/providers/ReadReferenceView.java

@@ -5,6 +5,8 @@ import net.sf.samtools.SAMSequenceRecord;
 import net.sf.samtools.util.StringUtil;
 import net.sf.picard.reference.ReferenceSequence;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
 /*
  * Copyright (c) 2009 The Broad Institute
  *
@@ -62,17 +64,7 @@ public class ReadReferenceView extends ReferenceView {
     public char[] getReferenceBases( SAMRecord read ) {
         if (read.getReadUnmappedFlag())
             return null;
-
+        return getReferenceBases( GenomeLocParser.createGenomeLoc(read) );
-        String contig = read.getReferenceName();
-        int start = read.getAlignmentStart();
-        int stop = read.getAlignmentEnd();
-
-        SAMSequenceRecord sequenceRecord = reference.getSequenceDictionary().getSequence(contig);
-        if (stop > sequenceRecord.getSequenceLength())
-            stop = sequenceRecord.getSequenceLength();
-
-        ReferenceSequence alignmentToReference = reference.getSubsequenceAt(contig, start, stop);
-        return ( StringUtil.bytesToString(alignmentToReference.getBases()) + Utils.dupString('X', read.getAlignmentEnd() - stop) ).toCharArray();
     }
 
 }

java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java

@@ -1,9 +1,15 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
 import org.broadinstitute.sting.utils.fasta.IndexedFastaSequenceFile;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.Utils;
 
 import java.util.Collections;
 import java.util.Collection;
+
+import net.sf.samtools.SAMSequenceRecord;
+import net.sf.samtools.util.StringUtil;
+import net.sf.picard.reference.ReferenceSequence;
 /**
  * User: hanna
  * Date: May 22, 2009
@@ -46,4 +52,18 @@ public class ReferenceView implements View {
     public void close() {
         reference = null;
     }
+
+    /**
+     * Allow the user to pull reference info from any arbitrary region of the reference.
+     * If parts of the reference don't exist, mark them in the char array with 'X'es.
+     * @param genomeLoc The locus.
+     * @return A list of the bases starting at the start of the locus (inclusive) and ending
+     *         at the end of the locus (inclusive).
+     */
+    protected char[] getReferenceBases( GenomeLoc genomeLoc ) {
+        SAMSequenceRecord sequenceInfo = reference.getSequenceDictionary().getSequence(genomeLoc.getContig());
+        long stop = Math.min( genomeLoc.getStop(), sequenceInfo.getSequenceLength() );
+        ReferenceSequence subsequence = reference.getSubsequenceAt(genomeLoc.getContig(),genomeLoc.getStart(),stop);
+        return (StringUtil.bytesToString(subsequence.getBases()) + Utils.dupString('X', (int)(genomeLoc.getStop() - stop)) ).toCharArray();        
+    }
 }

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

@@ -58,7 +58,7 @@ abstract public class BasicPileup implements Pileup {
     }
 
     public static ArrayList<Byte> basePileup( List<SAMRecord> reads, List<Integer> offsets ) {
-        ArrayList<Byte> bases = new ArrayList(reads.size());
+        ArrayList<Byte> bases = new ArrayList<Byte>(reads.size());
         for ( int i = 0; i < reads.size(); i++ ) {
             SAMRecord read = reads.get(i);
             int offset = offsets.get(i);
@@ -68,7 +68,7 @@ abstract public class BasicPileup implements Pileup {
     }
 
     public static ArrayList<Byte> qualPileup( List<SAMRecord> reads, List<Integer> offsets ) {
-        ArrayList<Byte> quals = new ArrayList(reads.size());
+        ArrayList<Byte> quals = new ArrayList<Byte>(reads.size());
         for ( int i = 0; i < reads.size(); i++ ) {
             SAMRecord read = reads.get(i);
             int offset = offsets.get(i);
@@ -79,7 +79,7 @@ abstract public class BasicPileup implements Pileup {
     }
 
     public static ArrayList<Byte> mappingQualPileup( List<SAMRecord> reads) {
-        ArrayList<Byte> quals = new ArrayList(reads.size());
+        ArrayList<Byte> quals = new ArrayList<Byte>(reads.size());
         for ( int i = 0; i < reads.size(); i++ ) {
             SAMRecord read = reads.get(i);
             byte qual = (byte)read.getMappingQuality();
@@ -349,10 +349,10 @@ abstract public class BasicPileup implements Pileup {
 
     public static byte consensusBase(String bases) {
         String canon = bases.toUpperCase();
-        int ACount = Utils.countOccurances('A', bases);
+        int ACount = Utils.countOccurrences('A', bases);
-        int CCount = Utils.countOccurances('C', bases);
+        int CCount = Utils.countOccurrences('C', bases);
-        int TCount = Utils.countOccurances('T', bases);
+        int TCount = Utils.countOccurrences('T', bases);
-        int GCount = Utils.countOccurances('G', bases);
+        int GCount = Utils.countOccurrences('G', bases);
 
         int m = Math.max(ACount, Math.max(CCount, Math.max(TCount, GCount)));
         if ( ACount == m ) return 'A';

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

@@ -437,12 +437,11 @@ public class Utils {
 
     public static String dupString( char c, int nCopies ) {
         char[] chars = new char[nCopies];
-        for ( int i = 0; i < nCopies; i++ ) chars[i] = c;
+        Arrays.fill(chars,c);
-        //System.out.printf("chars is %s%n", new String(chars));
         return new String(chars);
     }
 
-    public static int countOccurances(char c, String s) {
+    public static int countOccurrences(char c, String s) {
         int count = 0;
         for ( int i = 0; i < s.length(); i++ ) {
             count += s.charAt(i) == c ? 1 : 0;

java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java

@@ -247,7 +247,7 @@ public class DupUtils {
         String bases = BasicPileup.basePileupAsString(duplicates, offsets);
         ArrayList<Byte> quals = BasicPileup.qualPileup(duplicates, offsets);
         byte combinedBase  = BasicPileup.consensusBase(bases);
-        int baseMatches = Utils.countOccurances((char)combinedBase, bases);
+        int baseMatches = Utils.countOccurrences((char)combinedBase, bases);
         double maxP = QualityUtils.qualToProb(Utils.listMaxByte(quals));
         double mismatchRate = (double)baseMatches / bases.length();
         byte combinedQual = QualityUtils.probToQual(Math.min(maxP, mismatchRate), 0.0);

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

@@ -0,0 +1,59 @@
+/*
+ * Copyright (c) 2009 The Broad Institute
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils;
+
+import org.junit.Test;
+import junit.framework.Assert;
+
+/**
+ * Testing framework for general purpose utilities class.
+ *
+ * @author hanna
+ * @version 0.1
+ */
+
+public class UtilsTest {
+
+    @Test
+    public void testDupStringNoChars() {
+        String duped = Utils.dupString('a',0);
+        Assert.assertEquals("dupString did not produce zero-length string", 0, duped.length());
+    }
+
+    @Test
+    public void testDupStringOneChar() {
+        String duped = Utils.dupString('b',1);
+        Assert.assertEquals("dupString did not produce single character string", 1, duped.length());
+        Assert.assertEquals("dupString character was incorrect", 'b', duped.charAt(0));
+    }
+
+    @Test
+    public void testDupStringMultiChar() {
+        String duped = Utils.dupString('c',5);
+        Assert.assertEquals("dupString did not produce five character string", 5, duped.length());
+        Assert.assertEquals("dupString string was incorrect", "ccccc", duped);
+    }
+
+}