turned off the progress output from tribble when making an index, and fixing a case where the index file isn't writable so we instead make the index in memory.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3312 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java

@@ -120,7 +120,16 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
      */
     public static LinearIndex createIndex(File inputFile, FeatureCodec codec) throws IOException {
         LinearIndexCreator create = new LinearIndexCreator(inputFile, codec);
-        return create.createIndex();
+        create.setDisplayProgress(false);  // don't display progress indicators
+
+        // if we can write the index, we should, but if not just create it in memory
+        if (new File(inputFile.getAbsoluteFile() + linearIndexExtension).canWrite())
+            return create.createIndex();
+        else {
+            logger.info("Unable to write to location " + inputFile.getAbsoluteFile() + linearIndexExtension + " for index file, creating index in memory only");
+            return create.createIndex(null);
+        }
+
     }
 
     /**

java/src/org/broadinstitute/sting/utils/genotype/vcf/VCFReader.java

@@ -69,7 +69,7 @@ public class VCFReader implements Iterator<VCFRecord>, Iterable<VCFRecord> {
         }
         if (transform != null) codec.setTransformer(transform);
         try {
-            vcfReader = new FeatureReader(vcfFile,codec);
+            vcfReader = new FeatureReader(vcfFile,index,codec);
             iterator= vcfReader.iterator();
         } catch (FileNotFoundException e) {
             throw new StingException("Unable to read VCF File from " + vcfFile, e);

java/test/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilderUnitTest.java

@@ -23,10 +23,14 @@
 
 package org.broadinstitute.sting.gatk.refdata.tracks.builders;
 
+import org.broad.tribble.vcf.VCFCodec;
 import org.broadinstitute.sting.BaseTest;
+import org.junit.Assert;
 import org.junit.Before;
 import org.junit.Test;
 
+import java.io.File;
+import java.io.IOException;
 import java.util.Map;
 
 
@@ -49,9 +53,19 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
     @Test
     public void testBuilder() {
         Map<String,Class> classes = builder.getAvailableTrackNamesAndTypes();
-        for (String c: classes.keySet()) {
-            System.err.println("class = " + c);
+        Assert.assertTrue(classes.size() > 0);
+    }
+
+    @Test
+    public void testBuilderIndexUnwriteable() {
+        File vcfFile = new File(validationDataLocation + "/ROD_validation/mixedup.vcf");
+        try {
+            builder.createIndex(vcfFile,new VCFCodec());
+        } catch (IOException e) {
+            Assert.fail("Unable to make index because of IO exception " + e.getMessage());
         }
-        //Assert.fail("Fail");
+        // make sure we didn't write the file (check that it's length is zero)
+        Assert.assertEquals(0,new File(vcfFile + TribbleRMDTrackBuilder.linearIndexExtension).length());
+
     }
 }

settings/repository/org.broad/tribble-75.xml

@@ -1,3 +0,0 @@
-<ivy-module version="1.0">
-    <info organisation="org.broad" module="tribble" revision="75" status="integration" publication="20100503124200" />
-</ivy-module>

settings/repository/org.broad/tribble-77.xml

@@ -0,0 +1,3 @@
+<ivy-module version="1.0">
+    <info organisation="org.broad" module="tribble" revision="77" status="integration" publication="20100504124200" />
+</ivy-module>