From 11dbfc92a70e36702d293f2d417150cd93009afe Mon Sep 17 00:00:00 2001
From: Mark DePristo <depristo@broadinstitute.org>
Date: Fri, 22 Jun 2012 17:03:59 -0400
Subject: [PATCH] Horrible bugfix to decodeLoc() in BCF2Codec

-- Just completely wrong.
-- BCF2 shadowBCF now checks that the shadow bcf can be written to avoid /dev/null.bcf problem
-- Added samtools ex2.bcf file for decoding to our integrationtests
---
 .../sting/utils/codecs/bcf2/BCF2Codec.java    | 10 +--------
 .../sting/utils/codecs/bcf2/BCF2Utils.java    | 22 ++++++++++++++-----
 .../utils/codecs/vcf/VCFIntegrationTest.java  | 14 +++++++++---
 3 files changed, 28 insertions(+), 18 deletions(-)

diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
index 91331ac13..94c24b097 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
@@ -101,15 +101,7 @@ public final class BCF2Codec implements FeatureCodec<VariantContext>, ReferenceD
 
     @Override
     public Feature decodeLoc( final PositionalBufferedStream inputStream ) {
-        recordNo++;
-        final VariantContextBuilder builder = new VariantContextBuilder();
-
-        final int sitesBlockSize = decoder.readBlockSize(inputStream);
-        final int genotypeBlockSize = decoder.readBlockSize(inputStream); // necessary because it's in the stream
-        decoder.readNextBlock(sitesBlockSize, inputStream);
-        decodeSiteLoc(builder);
-
-        return builder.fullyDecoded(true).make();
+        return decode(inputStream);
     }
 
     @Override
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
index 51fbd3a7f..21deb4158 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
@@ -32,10 +32,7 @@ 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.io.OutputStream;
+import java.io.*;
 import java.util.*;
 
 /**
@@ -207,14 +204,27 @@ public final class BCF2Utils {
      * @return the BCF
      */
     @Requires("vcfFile != null")
-    @Ensures("result != null")
     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 {
             final File bcf = new File( path + ".bcf" );
-            return bcf.canWrite() ? bcf : null;
+            if ( bcf.canRead() )
+                return bcf;
+            else {
+                try {
+                    // this is the only way to robustly decide if we could actually write to BCF
+                    final FileOutputStream o = new FileOutputStream(bcf);
+                    o.close();
+                    bcf.delete();
+                    return bcf;
+                } catch ( FileNotFoundException e ) {
+                    return null;
+                } catch ( IOException e ) {
+                    return null;
+                }
+            }
         }
     }
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
index 3a5f2efe8..14b75fbc6 100644
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
@@ -30,7 +30,6 @@ public class VCFIntegrationTest extends WalkerTest {
     // See https://getsatisfaction.com/gsa/topics/support_vcf_4_1_structural_variation_breakend_alleles?utm_content=topic_link&utm_medium=email&utm_source=new_topic
     public void testReadingAndWritingBreakpointAlleles() {
         String testVCF = privateTestDir + "breakpoint-example.vcf";
-        //String testVCF = validationDataLocation + "multiallelic.vcf";
 
         String baseCommand = "-R " + b37KGReference + " --no_cmdline_in_header -o %s ";
 
@@ -51,11 +50,20 @@ public class VCFIntegrationTest extends WalkerTest {
     }
 
     @Test
-    public void testReadingAndWritingSamtoolsWExBCFExample() {
+    public void testWritingSamtoolsWExBCFExample() {
         String testVCF = privateTestDir + "ex2.vcf";
         String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
         String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
         WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("9773d6a121cfcb18d090965bc520f120"));
-        executeTest("Test reading and writing samtools WEx vcf/BCF example", spec1);
+        executeTest("Test writing samtools WEx BCF example", spec1);
+    }
+
+    @Test
+    public void testReadingSamtoolsWExBCFExample() {
+        String testVCF = privateTestDir + "ex2.bcf";
+        String baseCommand = "-R " + b36KGReference + " --no_cmdline_in_header -o %s ";
+        String test1 = baseCommand + "-T SelectVariants -V " + testVCF;
+        WalkerTestSpec spec1 = new WalkerTestSpec(test1, 1, Arrays.asList("63a2e0484ae37b0680514f53e0bf0c94"));
+        executeTest("Test reading samtools WEx BCF example", spec1);
     }
 }