Bugfixes and testdata cleanup

-- Cut down the size of a few large files in public/testdata that were only used in part
-- Refactor vcf Filename => shadow BCF filename to BCF2Utils.  Fix bug in WalkerTest due to the way this was handled previously

public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java

@@ -28,6 +28,7 @@ import net.sf.samtools.util.BlockCompressedOutputStream;
 import org.apache.log4j.Logger;
 import org.broad.tribble.AbstractFeatureReader;
 import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
+import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -105,7 +106,7 @@ public class VariantContextWriterStorage implements Storage<VariantContextWriter
         // if the stub says to test BCF, create a secondary writer to BCF and an 2 way out writer to send to both
         // TODO -- remove me when argument generateShadowBCF is removed
         if ( stub.alsoWriteBCFForTest() && ! VariantContextWriterFactory.isBCFOutput(file, options)) {
-            final File bcfFile = new File(file.getAbsolutePath().replace(".vcf", ".bcf"));
+            final File bcfFile = BCF2Utils.shadowBCF(file);
             VariantContextWriter bcfWriter = VariantContextWriterFactory.create(bcfFile, stub.getMasterSequenceDictionary(), options);
             writer = new TestWriter(writer, bcfWriter);
         }

public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java

@@ -30,6 +30,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFIDHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
+import java.io.File;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayList;
@@ -189,4 +190,21 @@ public class BCF2Utils {
     public static final boolean isCollapsedString(final String s) {
         return s.charAt(0) == ',';
     }
+
+    /**
+     * Returns a good name for a shadow BCF file for vcfFile.
+     *
+     * foo.vcf => foo.bcf
+     * foo.xxx => foo.xxx.bcf
+     *
+     * @param vcfFile
+     * @return
+     */
+    public static final File shadowBCF(final File vcfFile) {
+        final String path = vcfFile.getAbsolutePath();
+        if ( path.contains(".vcf") )
+            return new File(path.replace(".vcf", ".bcf"));
+        else
+            return new File( path + ".bcf" );
+    }
 }

public/java/test/org/broadinstitute/sting/WalkerTest.java

@@ -34,6 +34,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
 import org.broadinstitute.sting.utils.Utils;
+import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -60,7 +61,7 @@ public class WalkerTest extends BaseTest {
     }
 
     public void validateOutputBCFIfPossible(final String name, final File resultFile) {
-        final File bcfFile = new File(resultFile.getAbsolutePath().replace(".vcf", ".bcf"));
+        final File bcfFile = BCF2Utils.shadowBCF(resultFile);
         if ( bcfFile.exists() ) {
             logger.warn("Checking shadow BCF output file " + bcfFile + " against VCF file " + resultFile);
             try {

public/java/test/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java

@@ -41,16 +41,17 @@ public class FeatureToGATKFeatureIteratorUnitTest extends BaseTest {
     @Test
     @SuppressWarnings("unchecked")
     public void testCloseFilePointers() throws IOException {
+        final String chr = "20";
         IndexedFastaSequenceFile seq = new CachingIndexedFastaSequenceFile(new File(BaseTest.hg19Reference));
         GenomeLocParser parser = new GenomeLocParser(seq);
         File file = new File(validationDataLocation + "NA12878.hg19.example1.vcf");
         VCFCodec codec = new VCFCodec();
         TestFeatureReader reader = new TestFeatureReader(file.getAbsolutePath(), codec);
-        CheckableCloseableTribbleIterator<Feature> tribbleIterator = reader.query("20", 1, 100000);
+        CheckableCloseableTribbleIterator<Feature> tribbleIterator = reader.query(chr, 1, 100000);
         FeatureToGATKFeatureIterator gatkIterator = new FeatureToGATKFeatureIterator(parser, tribbleIterator, "test");
         Assert.assertTrue(gatkIterator.hasNext(), "GATK feature iterator does not have a next value.");
         GenomeLoc gatkLocation = gatkIterator.next().getLocation();
-        Assert.assertEquals(gatkLocation.getContig(), "20", "Instead of chr 20 rod iterator was at location " + gatkLocation);
+        Assert.assertEquals(gatkLocation.getContig(), chr, "Instead of chr 20 rod iterator was at location " + gatkLocation);
         Assert.assertFalse(tribbleIterator.isClosed(), "Tribble iterator is closed but should be still open.");
         gatkIterator.close();
         Assert.assertTrue(tribbleIterator.isClosed(), "Tribble iterator is open but should be now closed.");

public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWritersUnitTest.java

@@ -32,22 +32,22 @@ package org.broadinstitute.sting.utils.variantcontext.writer;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.SAMSequenceDictionary;
 import org.broad.tribble.FeatureCodec;
-import org.broad.tribble.FeatureCodecHeader;
-import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.codecs.bcf2.*;
+import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextTestProvider;
-import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-import java.io.*;
+import java.io.File;
-import java.util.*;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.EnumSet;
+import java.util.List;
 
 
 public class VariantContextWritersUnitTest extends BaseTest {