Examples with IndexedFastaSequenceFile htsjdk.samtools.reference.IndexedFastaSequenceFile used on opensource projects

Example 6 with IndexedFastaSequenceFile

use of htsjdk.samtools.reference.IndexedFastaSequenceFile in project gatk by broadinstitute.

the class GATKToolUnitTest method testBestSequenceDictionary_fromReadsAndReference.

@Test
public void testBestSequenceDictionary_fromReadsAndReference() throws Exception {
    final GATKTool tool = new TestGATKToolWithReads();
    final CommandLineParser clp = new CommandLineArgumentParser(tool);
    final File bamFile = new File(publicTestDir + "org/broadinstitute/hellbender/engine/reads_data_source_test1.bam");
    final String fastaFile = hg19MiniReference;
    final String[] args = { "-I", bamFile.getCanonicalPath(), "-R", fastaFile };
    clp.parseArguments(System.out, args);
    tool.onStartup();
    //read the dict back in and compare to reference dict
    final SAMSequenceDictionary toolDict = tool.getBestAvailableSequenceDictionary();
    final SAMSequenceDictionary fastaDict = new IndexedFastaSequenceFile(new File(fastaFile)).getSequenceDictionary();
    toolDict.assertSameDictionary(fastaDict);
    fastaDict.assertSameDictionary(toolDict);
    Assert.assertEquals(toolDict, fastaDict);
}

Example 7 with IndexedFastaSequenceFile

use of htsjdk.samtools.reference.IndexedFastaSequenceFile in project gatk by broadinstitute.

the class CachingIndexedFastaSequenceFileUnitTest method testSequential.

private void testSequential(final CachingIndexedFastaSequenceFile caching, final File fasta, final int querySize) throws FileNotFoundException {
    Assert.assertTrue(caching.isPreservingCase(), "testSequential only works for case preserving CachingIndexedFastaSequenceFile readers");
    final IndexedFastaSequenceFile uncached = new IndexedFastaSequenceFile(fasta);
    SAMSequenceRecord contig = uncached.getSequenceDictionary().getSequence(0);
    for (int i = 0; i < contig.getSequenceLength(); i += STEP_SIZE) {
        int start = i;
        int stop = start + querySize;
        if (stop <= contig.getSequenceLength()) {
            ReferenceSequence cachedVal = caching.getSubsequenceAt(contig.getSequenceName(), start, stop);
            ReferenceSequence uncachedVal = uncached.getSubsequenceAt(contig.getSequenceName(), start, stop);
            Assert.assertEquals(cachedVal.getName(), uncachedVal.getName());
            Assert.assertEquals(cachedVal.getContigIndex(), uncachedVal.getContigIndex());
            Assert.assertEquals(cachedVal.getBases(), uncachedVal.getBases());
        }
    }
    // asserts for efficiency.  We are going to make contig.length / STEP_SIZE queries
    // at each of range: start -> start + querySize against a cache with size of X.
    // we expect to hit the cache each time range falls within X.  We expect a hit
    // on the cache if range is within X.  Which should happen at least (X - query_size * 2) / STEP_SIZE
    // times.
    final int minExpectedHits = (int) Math.floor((Math.min(caching.getCacheSize(), contig.getSequenceLength()) - querySize * 2.0) / STEP_SIZE);
    caching.printEfficiency(Level.WARN);
    Assert.assertTrue(caching.getCacheHits() >= minExpectedHits, "Expected at least " + minExpectedHits + " cache hits but only got " + caching.getCacheHits());
}

Example 8 with IndexedFastaSequenceFile

use of htsjdk.samtools.reference.IndexedFastaSequenceFile in project gatk by broadinstitute.

the class IntervalUtilsUnitTest method invalidIntervalDataProvider.

@DataProvider(name = "invalidIntervalTestData")
public Object[][] invalidIntervalDataProvider() throws Exception {
    File fastaFile = new File(publicTestDir + "exampleFASTA.fasta");
    GenomeLocParser genomeLocParser = new GenomeLocParser(new IndexedFastaSequenceFile(fastaFile));
    return new Object[][] { new Object[] { genomeLocParser, "1", 10000000, 20000000 }, new Object[] { genomeLocParser, "2", 1, 2 }, new Object[] { genomeLocParser, "1", -1, 50 } };
}

Example 9 with IndexedFastaSequenceFile

use of htsjdk.samtools.reference.IndexedFastaSequenceFile in project gatk by broadinstitute.

the class IntervalUtilsUnitTest method negativeOneLengthIntervalDataProvider.

// TODO - remove once a corrected version of the exome interval list is released.
@DataProvider(name = "negativeOneLengthIntervalTestData")
public Object[][] negativeOneLengthIntervalDataProvider() throws Exception {
    File fastaFile = new File(publicTestDir + "exampleFASTA.fasta");
    GenomeLocParser genomeLocParser = new GenomeLocParser(new IndexedFastaSequenceFile(fastaFile));
    return new Object[][] { new Object[] { genomeLocParser, "1", 2, 1 }, new Object[] { genomeLocParser, "1", 500, 499 }, new Object[] { genomeLocParser, "1", 1000, 999 } };
}