{"action":"created","comment":{"url":"https://api.github.com/repos/broadinstitute/gatk/pulls/comments/216435515","pull_request_review_id":153915764,"id":216435515,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDIxNjQzNTUxNQ==","diff_hunk":"@@ -54,116 +60,109 @@ private static long getCacheSize(final long cacheSizeRequested) {\n         return cacheSizeRequested == -1 ? CachingIndexedFastaSequenceFile.DEFAULT_CACHE_SIZE : cacheSizeRequested;\n     }\n \n-    @Test(dataProvider = \"fastas\", enabled = ! DEBUG)\n-    public void testCachingIndexedFastaReaderSequential1(Path fasta, int cacheSize, int querySize) throws FileNotFoundException {\n-        final CachingIndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, getCacheSize(cacheSize), true, false);\n+    @Test(dataProvider = \"fastas\")\n+    public void testCachingIndexedFastaReaderSequential1(Path fasta, Path unzipped, int cacheSize, int querySize) throws IOException {\n+        try(final CachingIndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, getCacheSize(cacheSize), true, false)) {\n \n-        SAMSequenceRecord contig = caching.getSequenceDictionary().getSequence(0);\n-        logger.warn(String.format(\"Checking contig %s length %d with cache size %d and query size %d\",\n-                contig.getSequenceName(), contig.getSequenceLength(), cacheSize, querySize));\n-        testSequential(caching, fasta, querySize);\n+            SAMSequenceRecord contig = caching.getSequenceDictionary().getSequence(0);\n+            logger.warn(String.format(\"Checking contig %s length %d with cache size %d and query size %d\",\n+                                      contig.getSequenceName(), contig.getSequenceLength(), cacheSize, querySize));\n+            testSequential(caching, unzipped, querySize);\n+        }\n     }\n \n-    private void testSequential(final CachingIndexedFastaSequenceFile caching, final Path fasta, final int querySize) throws FileNotFoundException {\n+    private void testSequential(final CachingIndexedFastaSequenceFile caching, final Path unzipped, final int querySize) throws IOException {\n         Assert.assertTrue(caching.isPreservingCase(), \"testSequential only works for case preserving CachingIndexedFastaSequenceFile readers\");\n \n-        final IndexedFastaSequenceFile uncached = new IndexedFastaSequenceFile(fasta);\n+        //use an unzipped version of the fasta because it's slow to repeatedly query the zipped version without caching\n+        try( final ReferenceSequenceFile uncached = ReferenceSequenceFileFactory.getReferenceSequenceFile(unzipped)) {\n \n-        SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0);\n-        for ( int i = 0; i < contig.getSequenceLength(); i += STEP_SIZE ) {\n-            int start = i;\n-            int stop = start + querySize;\n-            if ( stop <= contig.getSequenceLength() ) {\n-                ReferenceSequence cachedVal = caching.getSubsequenceAt(contig.getSequenceName(), start, stop);\n-                ReferenceSequence uncachedVal = uncached.getSubsequenceAt(contig.getSequenceName(), start, stop);\n+            SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0);\n+            for (int i = 0; i < contig.getSequenceLength(); i += STEP_SIZE) {\n+                int start = i;\n+                int stop = start + querySize;\n+                if (stop <= contig.getSequenceLength()) {\n+                    ReferenceSequence cachedVal = caching.getSubsequenceAt(contig.getSequenceName(), start, stop);\n+                    ReferenceSequence uncachedVal = uncached.getSubsequenceAt(contig.getSequenceName(), start, stop);\n \n-                Assert.assertEquals(cachedVal.getName(), uncachedVal.getName());\n-                Assert.assertEquals(cachedVal.getContigIndex(), uncachedVal.getContigIndex());\n-                Assert.assertEquals(cachedVal.getBases(), uncachedVal.getBases());\n+                    Assert.assertEquals(cachedVal.getName(), uncachedVal.getName());\n+                    Assert.assertEquals(cachedVal.getContigIndex(), uncachedVal.getContigIndex());\n+                    Assert.assertEquals(cachedVal.getBases(), uncachedVal.getBases());\n+                }\n             }\n-        }\n \n-        // asserts for efficiency.  We are going to make contig.length / STEP_SIZE queries\n-        // at each of range: start -> start + querySize against a cache with size of X.\n-        // we expect to hit the cache each time range falls within X.  We expect a hit\n-        // on the cache if range is within X.  Which should happen at least (X - query_size * 2) / STEP_SIZE\n-        // times.\n-        final int minExpectedHits = (int)Math.floor((Math.min(caching.getCacheSize(), contig.getSequenceLength()) - querySize * 2.0) / STEP_SIZE);\n-        caching.printEfficiency(Level.WARN);\n-        Assert.assertTrue(caching.getCacheHits() >= minExpectedHits, \"Expected at least \" + minExpectedHits + \" cache hits but only got \" + caching.getCacheHits());\n+            // asserts for efficiency.  We are going to make contig.length / STEP_SIZE queries\n+            // at each of range: start -> start + querySize against a cache with size of X.\n+            // we expect to hit the cache each time range falls within X.  We expect a hit\n+            // on the cache if range is within X.  Which should happen at least (X - query_size * 2) / STEP_SIZE\n+            // times.\n+            final int minExpectedHits = (int) Math.floor(\n+                    (Math.min(caching.getCacheSize(), contig.getSequenceLength()) - querySize * 2.0) / STEP_SIZE);\n+            caching.printEfficiency(Level.WARN);\n+            Assert.assertTrue(caching.getCacheHits() >= minExpectedHits,\n+                              \"Expected at least \" + minExpectedHits + \" cache hits but only got \" + caching.getCacheHits());\n+        }\n \n     }\n \n     // Tests grabbing sequences around a middle cached value.\n-    @Test(dataProvider = \"fastas\", enabled = ! DEBUG)\n-    public void testCachingIndexedFastaReaderTwoStage(Path fasta, int cacheSize, int querySize) throws FileNotFoundException {\n-        final IndexedFastaSequenceFile uncached = new IndexedFastaSequenceFile(fasta);\n-        final CachingIndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, getCacheSize(cacheSize), true, false);\n-\n-        SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0);\n-\n-        int middleStart = (contig.getSequenceLength() - querySize) / 2;\n-        int middleStop = middleStart + querySize;\n-\n-        logger.warn(String.format(\"Checking contig %s length %d with cache size %d and query size %d with intermediate query\",\n-                contig.getSequenceName(), contig.getSequenceLength(), cacheSize, querySize));\n-\n-        for ( int i = 0; i < contig.getSequenceLength(); i += 10 ) {\n-            int start = i;\n-            int stop = start + querySize;\n-            if ( stop <= contig.getSequenceLength() ) {\n-                ReferenceSequence grabMiddle = caching.getSubsequenceAt(contig.getSequenceName(), middleStart, middleStop);\n-                ReferenceSequence cachedVal = caching.getSubsequenceAt(contig.getSequenceName(), start, stop);\n-                ReferenceSequence uncachedVal = uncached.getSubsequenceAt(contig.getSequenceName(), start, stop);\n-\n-                Assert.assertEquals(cachedVal.getName(), uncachedVal.getName());\n-                Assert.assertEquals(cachedVal.getContigIndex(), uncachedVal.getContigIndex());\n-                Assert.assertEquals(cachedVal.getBases(), uncachedVal.getBases());\n-            }\n-        }\n-    }\n-\n-    @DataProvider(name = \"ParallelFastaTest\")\n-    public Object[][] createParallelFastaTest() {\n-        List<Object[]> params = new ArrayList<>();\n-\n-        for ( Path fasta : Arrays.asList(simpleFasta) ) {\n-            for ( int cacheSize : CACHE_SIZES ) {\n-                for ( int querySize : QUERY_SIZES ) {\n-                    for ( int nt : Arrays.asList(1, 2, 3, 4) ) {\n-                        params.add(new Object[]{fasta, cacheSize, querySize, nt});\n-                    }\n+    @Test(dataProvider = \"fastas\")\n+    public void testCachingIndexedFastaReaderTwoStage(Path fasta, Path unzipped, int cacheSize, int querySize) throws IOException {\n+        try(final ReferenceSequenceFile uncached = ReferenceSequenceFileFactory.getReferenceSequenceFile(unzipped);\n+            final CachingIndexedFastaSequenceFile caching = new CachingIndexedFastaSequenceFile(fasta, getCacheSize(cacheSize), true, false)) {\n+\n+            SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0);\n+\n+            int middleStart = (contig.getSequenceLength() - querySize) / 2;\n+            int middleStop = middleStart + querySize;\n+\n+            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