Examples with SAMException htsjdk.samtools.SAMException used on opensource projects

Example 1 with SAMException

use of htsjdk.samtools.SAMException in project gatk by broadinstitute.

the class BedToIntervalListTest method doTest.

private void doTest(final String inputBed, final String header) throws IOException {
    final File outputFile = BaseTest.createTempFile("bed_to_interval_list_test.", ".interval_list");
    final BedToIntervalList program = new BedToIntervalList();
    final File inputBedFile = new File(TEST_DATA_DIR, inputBed);
    program.INPUT = inputBedFile;
    program.SEQUENCE_DICTIONARY = new File(TEST_DATA_DIR, header);
    program.OUTPUT = outputFile;
    program.doWork();
    // Assert they are equal
    SAMException unexpectedException = null;
    try {
        IOUtil.assertFilesEqual(new File(inputBedFile.getAbsolutePath() + ".interval_list"), outputFile);
    } catch (final SAMException e) {
        unexpectedException = e;
    }
    Assert.assertEquals(unexpectedException, null);
}

Example 2 with SAMException

use of htsjdk.samtools.SAMException in project gatk by broadinstitute.

the class BuildBamIndex method doWork.

/**
     * Main method for the program.  Checks that all input files are present and
     * readable and that the output file can be written to.  Then iterates through
     * all the records generating a BAM Index, then writes the bai file.
     */
@Override
protected Object doWork() {
    try {
        inputUrl = new URL(INPUT);
    } catch (MalformedURLException e) {
        inputFile = new File(INPUT);
    }
    // set default output file - input-file.bai
    if (OUTPUT == null) {
        final String baseFileName;
        if (inputUrl != null) {
            final String path = inputUrl.getPath();
            final int lastSlash = path.lastIndexOf('/');
            baseFileName = path.substring(lastSlash + 1, path.length());
        } else {
            baseFileName = inputFile.getAbsolutePath();
        }
        if (baseFileName.endsWith(BamFileIoUtils.BAM_FILE_EXTENSION)) {
            final int index = baseFileName.lastIndexOf('.');
            OUTPUT = new File(baseFileName.substring(0, index) + BAMIndex.BAMIndexSuffix);
        } else {
            OUTPUT = new File(baseFileName + BAMIndex.BAMIndexSuffix);
        }
    }
    IOUtil.assertFileIsWritable(OUTPUT);
    final SamReader bam;
    if (inputUrl != null) {
        // remote input
        bam = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).disable(SamReaderFactory.Option.EAGERLY_DECODE).enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS).open(SamInputResource.of(inputUrl));
    } else {
        // input from a normal file
        IOUtil.assertFileIsReadable(inputFile);
        bam = SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).enable(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS).open(inputFile);
    }
    if (bam.type() != SamReader.Type.BAM_TYPE) {
        throw new SAMException("Input file must be bam file, not sam file.");
    }
    if (!bam.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.coordinate)) {
        throw new SAMException("Input bam file must be sorted by coordinates");
    }
    BAMIndexer.createIndex(bam, OUTPUT);
    logger.info("Successfully wrote bam index file " + OUTPUT);
    CloserUtil.close(bam);
    return null;
}

Example 3 with SAMException

use of htsjdk.samtools.SAMException in project gatk by broadinstitute.

the class CachingIndexedFastaSequenceFile method getSubsequenceAt.

/**
     * Gets the subsequence of the contig in the range [start,stop]
     *
     * Uses the sequence cache if possible, or updates the cache to handle the request.  If the range
     * is larger than the cache itself, just loads the sequence directly, not changing the cache at all
     *
     * @param contig Contig whose subsequence to retrieve.
     * @param start inclusive, 1-based start of region.
     * @param stop inclusive, 1-based stop of region.
     * @return The partial reference sequence associated with this range.  If preserveCase is false, then
     *         all of the bases in the ReferenceSequence returned by this method will be upper cased.
     */
@Override
public ReferenceSequence getSubsequenceAt(final String contig, long start, final long stop) {
    final ReferenceSequence result;
    if ((stop - start) >= cacheSize) {
        cacheMisses++;
        result = super.getSubsequenceAt(contig, start, stop);
        if (!preserveCase)
            StringUtil.toUpperCase(result.getBases());
        if (!preserveIUPAC)
            BaseUtils.convertIUPACtoN(result.getBases(), true, start < 1);
    } else {
        // todo -- potential optimization is to check if contig.name == contig, as this in general will be true
        SAMSequenceRecord contigInfo = super.getSequenceDictionary().getSequence(contig);
        if (contigInfo == null) {
            throw new UserException.MissingContigInSequenceDictionary(contig, super.getSequenceDictionary());
        }
        if (stop > contigInfo.getSequenceLength())
            throw new SAMException("Query asks for data past end of contig. Query contig " + contig + " start:" + start + " stop:" + stop + " contigLength:" + contigInfo.getSequenceLength());
        if (start < cache.start || stop > cache.stop || cache.seq == null || cache.seq.getContigIndex() != contigInfo.getSequenceIndex()) {
            cacheMisses++;
            cache.start = Math.max(start - cacheMissBackup, 0);
            cache.stop = Math.min(start + cacheSize + cacheMissBackup, contigInfo.getSequenceLength());
            cache.seq = super.getSubsequenceAt(contig, cache.start, cache.stop);
            // convert all of the bases in the sequence to upper case if we aren't preserving cases
            if (!preserveCase)
                StringUtil.toUpperCase(cache.seq.getBases());
            if (!preserveIUPAC)
                BaseUtils.convertIUPACtoN(cache.seq.getBases(), true, cache.start == 0);
        } else {
            cacheHits++;
        }
        // at this point we determine where in the cache we want to extract the requested subsequence
        final int cacheOffsetStart = (int) (start - cache.start);
        final int cacheOffsetStop = (int) (stop - start + cacheOffsetStart + 1);
        try {
            result = new ReferenceSequence(cache.seq.getName(), cache.seq.getContigIndex(), Arrays.copyOfRange(cache.seq.getBases(), cacheOffsetStart, cacheOffsetStop));
        } catch (ArrayIndexOutOfBoundsException e) {
            throw new GATKException(String.format("BUG: bad array indexing.  Cache start %d and end %d, request start %d end %d, offset start %d and end %d, base size %d", cache.start, cache.stop, start, stop, cacheOffsetStart, cacheOffsetStop, cache.seq.getBases().length), e);
        }
    }
    // for debugging -- print out our efficiency if requested
    if (PRINT_EFFICIENCY && (getCacheHits() + getCacheMisses()) % PRINT_FREQUENCY == 0)
        printEfficiency(Level.INFO);
    return result;
}