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

public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java

@@ -18,6 +18,7 @@ import java.util.zip.GZIPInputStream;
 
 
 public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
+    public final static int MAX_ALLELE_SIZE_BEFORE_WARNING = (int)Math.pow(2, 20);
 
     protected final static Logger log = Logger.getLogger(VCFCodec.class);
     protected final static int NUM_STANDARD_FIELDS = 8;  // INFO is the 8th column
@@ -252,7 +253,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
 
         // if we have don't have a header, or we have a header with no genotyping data check that we have eight columns.  Otherwise check that we have nine (normal colummns + genotyping data)
         if (( (header == null || !header.hasGenotypingData()) && nParts != NUM_STANDARD_FIELDS) ||
-             (header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
+                (header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
             throw new UserException.MalformedVCF("there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
                     " tokens, and saw " + nParts + " )", lineNo);
 
@@ -518,8 +519,11 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
      * @param lineNo  the line number for this record
      */
     private static void checkAllele(String allele, boolean isRef, int lineNo) {
-	if ( allele == null || allele.length() == 0 )
+        if ( allele == null || allele.length() == 0 )
-	    generateException("Empty alleles are not permitted in VCF records", lineNo);
+            generateException("Empty alleles are not permitted in VCF records", lineNo);
+
+        if ( MAX_ALLELE_SIZE_BEFORE_WARNING != -1 && allele.length() > MAX_ALLELE_SIZE_BEFORE_WARNING )
+            log.warn(String.format("Allele detected with length %d exceeding max size %d at approximately line %d, likely resulting in degraded VCF processing performance", allele.length(), MAX_ALLELE_SIZE_BEFORE_WARNING, lineNo));
 
         if ( isSymbolicAllele(allele) ) {
             if ( isRef ) {
@@ -572,12 +576,13 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
 
     public static int computeForwardClipping(List<Allele> unclippedAlleles, String ref) {
         boolean clipping = true;
+        final byte ref0 = (byte)ref.charAt(0);
 
         for ( Allele a : unclippedAlleles ) {
             if ( a.isSymbolic() )
                 continue;
 
-            if ( a.length() < 1 || (a.getBases()[0] != ref.getBytes()[0]) ) {
+            if ( a.length() < 1 || (a.getBases()[0] != ref0) ) {
                 clipping = false;
                 break;
             }
@@ -604,7 +609,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
                     stillClipping = false;
                 else if ( ref.length() == clipping )
                     generateException("bad alleles encountered", lineNo);
-                else if ( a.getBases()[a.length()-clipping-1] != ref.getBytes()[ref.length()-clipping-1] )
+                else if ( a.getBases()[a.length()-clipping-1] != ((byte)ref.charAt(ref.length()-clipping-1)) )
                     stillClipping = false;
             }
             if ( stillClipping )
@@ -613,6 +618,7 @@ public abstract class AbstractVCFCodec implements FeatureCodec, NameAwareCodec {
 
         return clipping;
     }
+
     /**
      * clip the alleles, based on the reference
      *

public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFCodecUnitTest.java

@@ -0,0 +1,91 @@
+/*
+ * Copyright (c) 2012, 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.
+ */
+
+// our package
+package org.broadinstitute.sting.utils.codecs.vcf;
+
+
+// the imports for unit testing.
+
+
+import org.broadinstitute.sting.BaseTest;
+import org.broadinstitute.sting.utils.variantcontext.*;
+import org.testng.Assert;
+import org.testng.annotations.BeforeSuite;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.util.*;
+
+
+public class VCFCodecUnitTest extends BaseTest {
+
+    // --------------------------------------------------------------------------------
+    //
+    // Provider
+    //
+    // --------------------------------------------------------------------------------
+
+    private class AlleleClippingTestProvider extends TestDataProvider {
+        final String ref;
+        final List<Allele> alleles = new ArrayList<Allele>();
+        final int expectedClip;
+
+        private AlleleClippingTestProvider(final int expectedClip, final String ref, final String ... alleles) {
+            super(AlleleClippingTestProvider.class);
+            this.ref = ref;
+            for ( final String allele : alleles )
+                this.alleles.add(Allele.create(allele));
+            this.expectedClip = expectedClip;
+        }
+
+        @Override
+        public String toString() {
+            return String.format("ref=%s allele=%s reverse clip %d", ref, alleles, expectedClip);
+        }
+    }
+
+    @DataProvider(name = "AlleleClippingTestProvider")
+    public Object[][] MakeAlleleClippingTest() {
+        // pair clipping
+        new AlleleClippingTestProvider(0, "ATT", "CCG");
+        new AlleleClippingTestProvider(1, "ATT", "CCT");
+        new AlleleClippingTestProvider(2, "ATT", "CTT");
+        new AlleleClippingTestProvider(2, "ATT", "ATT");  // cannot completely clip allele
+
+        // triplets
+        new AlleleClippingTestProvider(0, "ATT", "CTT", "CGG");
+        new AlleleClippingTestProvider(1, "ATT", "CTT", "CGT"); // the T can go
+        new AlleleClippingTestProvider(2, "ATT", "CTT", "CTT"); // both Ts can go
+
+        return AlleleClippingTestProvider.getTests(AlleleClippingTestProvider.class);
+    }
+
+
+    @Test(dataProvider = "AlleleClippingTestProvider")
+    public void TestAlleleClipping(AlleleClippingTestProvider cfg) {
+        int result = AbstractVCFCodec.computeReverseClipping(cfg.alleles, cfg.ref, 0, 1);
+        Assert.assertEquals(result, cfg.expectedClip);
+    }
+}

settings/repository/org.broad/tribble-53.xml

@@ -1,3 +1,3 @@
 <ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="46" status="integration" />
+    <info organisation="org.broad" module="tribble" revision="53" status="integration" />
 </ivy-module>