Don't allow the use of compressed (.gz) references in the GATK.

broadgsa · Mar 5, 2013 · 5e89f01 · 5e89f01
1 parent 7e1bfd6
commit 5e89f01
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Showing 2 changed files with 8 additions and 12 deletions.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java b/public/java/src/org/broadinstitute/sting/gatk/datasources/reference/ReferenceDataSource.java
@@ -67,18 +67,20 @@ public ReferenceDataSource(File fastaFile) {
             throw new UserException("The fasta file you specified (" + fastaFile.getAbsolutePath() + ") does not exist.");
 
         final boolean isGzipped = fastaFile.getAbsolutePath().endsWith(".gz");
+        if ( isGzipped ) {
+            throw new UserException.CannotHandleGzippedRef();
+        }
 
         final File indexFile = new File(fastaFile.getAbsolutePath() + ".fai");
 
         // determine the name for the dict file
-        final String fastaExt = (fastaFile.getAbsolutePath().endsWith("fa") ? ".fa" : ".fasta" ) + (isGzipped ? ".gz" : "");
+        final String fastaExt = fastaFile.getAbsolutePath().endsWith("fa") ? ".fa" : ".fasta";
         final File dictFile = new File(fastaFile.getAbsolutePath().replace(fastaExt, ".dict"));
 
         /*
         * if index file does not exist, create it manually
         */
         if (!indexFile.exists()) {
-            if ( isGzipped ) throw new UserException.CouldNotCreateReferenceFAIorDictForGzippedRef(fastaFile);
 
             logger.info(String.format("Index file %s does not exist. Trying to create it now.", indexFile.getAbsolutePath()));
             FSLockWithShared indexLock = new FSLockWithShared(indexFile,true);
@@ -115,7 +117,6 @@ public ReferenceDataSource(File fastaFile) {
         * This has been filed in trac as (PIC-370) Want programmatic interface to CreateSequenceDictionary
         */
         if (!dictFile.exists()) {
-            if ( isGzipped ) throw new UserException.CouldNotCreateReferenceFAIorDictForGzippedRef(fastaFile);
 
             logger.info(String.format("Dict file %s does not exist. Trying to create it now.", dictFile.getAbsolutePath()));
 

diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -387,15 +387,10 @@ public CouldNotCreateReferenceIndexFile(File f, String message, Exception e) {
         }
     }
 
-    public static class CouldNotCreateReferenceFAIorDictForGzippedRef extends UserException {
-        public CouldNotCreateReferenceFAIorDictForGzippedRef(final File f) {
-            super("Although the GATK can process .gz reference sequences, it currently cannot create FAI " +
-                    "or DICT files for them.  In order to use the GATK with reference.fasta.gz you will need to " +
-                    "create .dict and .fai files for reference.fasta.gz and name them reference.fasta.gz.fai and " +
-                    "reference.dict.  Potentially the easiest way to do this is to uncompress reference.fasta, " +
-                    "run the GATK to create the .dict and .fai files, and copy them to the appropriate location. " +
-                    "Sorry for the inconvenience.");
-        }
+    public static class CannotHandleGzippedRef extends UserException {
+	public CannotHandleGzippedRef() {
+	    super("The GATK cannot process compressed (.gz) reference sequences. Please unzip the file and try again.  Sorry for the inconvenience.");
+	}
     }
 
     public static class CouldNotCreateReferenceIndexFileBecauseOfLock extends UserException.CouldNotCreateReferenceIndexFile {