Package htsjdk.samtools.reference

Examples of htsjdk.samtools.reference.ReferenceSequenceFile

136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
        if (!ASSUME_SORTED && sam.getFileHeader().getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
            throw new PicardException("Header of input file " + INPUT.getAbsolutePath() + " indicates that it is not coordinate sorted.  " +
            "If you believe the records are in coordinate order, pass option ASSUME_SORTED=true.  If not, sort the file with SortSam.");
        }
        final PeekableIterator<SAMRecord> iterator = new PeekableIterator<SAMRecord>(sam.iterator());
        final ReferenceSequenceFile referenceFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE_SEQUENCE);

        {
            // Check that the sequence dictionaries match if present
            final SAMSequenceDictionary referenceDictionary= referenceFile.getSequenceDictionary();
            final SAMSequenceDictionary samFileDictionary = sam.getFileHeader().getSequenceDictionary();
            if (referenceDictionary != null && samFileDictionary != null) {
                SequenceUtil.assertSequenceDictionariesEqual(referenceDictionary, samFileDictionary);
            }
        }

        ////////////////////////////////////////////////////////////////////////////
        // Loop over the reference and the reads and calculate the basic metrics
        ////////////////////////////////////////////////////////////////////////////
        ReferenceSequence ref = null;
        final ProgressLogger
                progress = new ProgressLogger(log);
        while ((ref = referenceFile.nextSequence()) != null) {
            final byte[] refBases = ref.getBases();
            StringUtil.toUpperCase(refBases);
            final int refLength = refBases.length;
            final int lastWindowStart = refLength - WINDOW_SIZE;
View Full Code Here
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
        IOUtil.assertFileIsReadable(INTERVAL_LIST);
        IOUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
        IOUtil.assertFileIsWritable(OUTPUT);

        final IntervalList intervals = IntervalList.fromFile(INTERVAL_LIST);
        final ReferenceSequenceFile ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE_SEQUENCE);
        SequenceUtil.assertSequenceDictionariesEqual(intervals.getHeader().getSequenceDictionary(), ref.getSequenceDictionary());

        final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT);

        for (final Interval interval : intervals) {
            final ReferenceSequence seq = ref.getSubsequenceAt(interval.getSequence(), interval.getStart(), interval.getEnd());
            final byte[] bases = seq.getBases();
            if (interval.isNegativeStrand()) SequenceUtil.reverseComplement(bases);

            try {
                out.write(">");
View Full Code Here
83
84
85
86
87
88
89
90
91
92
93
    @Override
    protected int doWork() {
        IOUtil.assertFileIsReadable(REFERENCE);
        IOUtil.assertFileIsWritable(OUTPUT);

        final ReferenceSequenceFile refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE, true);

        // get the intervals
        final IntervalList intervals = segregateReference(refFile, MAX_TO_MERGE);

        log.info(String.format("Found %d intervals in %d loci during %s seconds", intervalProgress.getCount(), locusProgress.getCount(), locusProgress.getElapsedSeconds()));
View Full Code Here
94
95
96
97
98
99
100
101
102
103
104
105
        IOUtil.assertFileIsReadable(REFERENCE);
        IOUtil.assertFileIsWritable(OUTPUT);

        final SAMFileReader in = new SAMFileReader(INPUT);

        ReferenceSequenceFile reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE);
        SAMSequenceDictionary refDict = reference.getSequenceDictionary();

        if (refDict == null) {
          log.error("No reference sequence dictionary found. Aborting.  You can create a sequence dictionary for the reference fasta using CreateSequenceDictionary.jar.");
          in.close();
          return 1;
View Full Code Here
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
     * Read all the sequences from the given reference file, and convert into SAMSequenceRecords
     * @param referenceFile fasta or fasta.gz
     * @return SAMSequenceRecords containing info from the fasta, plus from cmd-line arguments.
     */
    SAMSequenceDictionary makeSequenceDictionary(final File referenceFile) {
        final ReferenceSequenceFile refSeqFile =
                ReferenceSequenceFileFactory.getReferenceSequenceFile(referenceFile, TRUNCATE_NAMES_AT_WHITESPACE);
        ReferenceSequence refSeq;
        final List<SAMSequenceRecord> ret = new ArrayList<SAMSequenceRecord>();
        final Set<String> sequenceNames = new HashSet<String>();
        for (int numSequences = 0; numSequences < NUM_SEQUENCES && (refSeq = refSeqFile.nextSequence()) != null; ++numSequences) {
            if (sequenceNames.contains(refSeq.getName())) {
                throw new PicardException("Sequence name appears more than once in reference: " + refSeq.getName());
            }
            sequenceNames.add(refSeq.getName());
            ret.add(makeSequenceRecord(refSeq));
View Full Code Here
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
        if (INPUT.getAbsoluteFile().equals(OUTPUT.getAbsoluteFile())) {
            throw new IllegalArgumentException("Input and output cannot be the same file.");
        }

        final ReferenceSequenceFile ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(INPUT, TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE);
        final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT);

        ReferenceSequence seq = null;
        while ((seq = ref.nextSequence()) != null) {
            final String name  = seq.getName();
            final byte[] bases = seq.getBases();

            try {
                out.write(">");
View Full Code Here
104
105
106
107
108
109
110
111
112
113
114
    }

    @Override
    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        ReferenceSequenceFile reference = null;
        if (REFERENCE_SEQUENCE != null) {
            IOUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
            reference = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE_SEQUENCE);

        }
View Full Code Here
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
        SequenceUtil.assertSequenceDictionariesEqual(
                reader.getFileHeader().getSequenceDictionary(),
                getProbeIntervals().getHeader().getSequenceDictionary()
        );

        ReferenceSequenceFile ref = null;
        if (REFERENCE_SEQUENCE != null) {
            IOUtil.assertFileIsReadable(REFERENCE_SEQUENCE);
            ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(REFERENCE_SEQUENCE);
            SequenceUtil.assertSequenceDictionariesEqual(
                    reader.getFileHeader().getSequenceDictionary(), ref.getSequenceDictionary(),
                    INPUT, REFERENCE_SEQUENCE
            );
        }

        final COLLECTOR collector = makeCollector(
View Full Code Here
108
109
110
111
112
113
114
115
116
117
118
        final SAMSequenceRecord record = new SAMSequenceRecord("fake1", referenceString.length());
        final SAMSequenceDictionary dictionary = new SAMSequenceDictionary();
        dictionary.addSequence(record);

        final ReferenceSequenceFile reference = new ReferenceSequenceFile() {

            boolean done = false;

            @Override
            public SAMSequenceDictionary getSequenceDictionary() {
View Full Code Here
TOP

Related Classes of htsjdk.samtools.reference.ReferenceSequenceFile

  • org.broadinstitute.gatk.engine.alignment.reference.bwt.BWTSupplementaryFileGenerator
  • org.broadinstitute.gatk.engine.alignment.reference.bwt.CreateBWTFromReference
  • org.broadinstitute.gatk.engine.alignment.reference.packing.CreatePACFromReference
  • org.broadinstitute.gatk.engine.datasources.providers.LocusViewTemplate
  • org.broadinstitute.gatk.tools.CatVariants
  • org.broadinstitute.gatk.tools.walkers.readutils.ClipReads
  • org.broadinstitute.gatk.utils.activeregion.ActivityProfileUnitTest
  • org.broadinstitute.gatk.utils.activeregion.BandPassActivityProfileUnitTest
  • org.broadinstitute.gatk.utils.interval.IntervalUtilsUnitTest
  • picard.analysis.CollectGcBiasMetrics
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.