From f3e2aae570b9d0df16d34051ac8cd3d8c9867090 Mon Sep 17 00:00:00 2001
From: aaron <aaron@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 25 May 2010 04:44:46 +0000
Subject: [PATCH] add experimental support for tabix files (for any of our
 Tribble rod types), as long as they end in .gz and can be read by the tabix
 reader.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3429 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../builders/TribbleRMDTrackBuilder.java      | 34 +++++++++++++++++++
 1 file changed, 34 insertions(+)

diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
index ceb4aed07..8dd4bfab7 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
@@ -105,6 +105,40 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
      */
     public FeatureReader createFeatureReader(Class targetClass, File inputFile) {
         FeatureReader reader = null;
+        if (inputFile.getAbsolutePath().endsWith(".gz"))
+            reader = createBasicFeatureReaderNoAssumedIndex(targetClass, inputFile);
+        else
+            reader = getLinearFeatureReader(targetClass, inputFile);
+        return reader;
+    }
+
+    /**
+     * create a feature reader, without assuming there exists an index.  This code assumes the feature
+     * reader of the appropriate type will figure out what the right index type is, and determine if it
+     * exists.
+     *
+     * @param targetClass the codec class type
+     * @param inputFile the file to load
+     * @return a feature reader implementation
+     */
+    private BasicFeatureReader createBasicFeatureReaderNoAssumedIndex(Class targetClass, File inputFile) {
+        // we might not know the index type, try loading with the default reader constructor
+        logger.debug("Attempting to blindly load " + inputFile);
+        try {
+            return new BasicFeatureReader(inputFile.getAbsolutePath(),this.createByType(targetClass));
+        } catch (IOException e) {
+            throw new StingException("Unable to create feature reader from file " + inputFile);
+        }
+    }
+
+    /**
+     * create a linear feature reader, where we create the index ahead of time
+     * @param targetClass the target class
+     * @param inputFile the tribble file to parse
+     * @return the input file as a FeatureReader
+     */
+    private FeatureReader getLinearFeatureReader(Class targetClass, File inputFile) {
+        FeatureReader reader;
         try {
             Index index = loadIndex(inputFile, this.createByType(targetClass), true);
             reader = new BasicFeatureReader(inputFile.getAbsolutePath(), index, this.createByType(targetClass));