Package htsjdk.samtools

Examples of htsjdk.samtools.SAMFileHeader

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    public SAMFileHeader getHeader() {
        if (samFiles.length == 0) {
            return null;
        }
        SAMFileReader reader = new SAMFileReader(samFiles[0]);
        SAMFileHeader header = reader.getFileHeader();
        reader.close();
        ;
        return header;
    }
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    private SAMFileHeader loadHeaders(){
        List<SAMFileHeader> headersList = new ArrayList<SAMFileHeader>();
        SAMFileHeader.SortOrder sortOrder = null;
        for(AlignmentReader reader: readers){
            SAMFileHeader curHeader = reader.getFileHeader();
            if(curHeader != null) {
                headersList.add(curHeader);
                sortOrder = curHeader.getSortOrder();
            }
        }
        if(sortOrder != null){
            SamFileHeaderMerger headerMerger = new SamFileHeaderMerger(sortOrder, headersList, true);
            return headerMerger.getMergedHeader();
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        return indexFile != null && indexFile.exists();
    }

    public List<String> getSequenceNames() {
        if (sequenceNames == null) {
            SAMFileHeader header = getFileHeader();
            if (header == null) {
                return null;
            }
            sequenceNames = new ArrayList();
            List<SAMSequenceRecord> records = header.getSequenceDictionary().getSequences();
            if (records.size() > 0) {
                for (SAMSequenceRecord rec : header.getSequenceDictionary().getSequences()) {
                    String chr = rec.getSequenceName();
                    sequenceNames.add(chr);
                }
            }
        }
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                    record.getMateNegativeStrandFlag(),
                    record.getMateUnmappedFlag()));
        }

        String keySequence = null;
        SAMFileHeader header = record.getHeader();
        String flowOrder = null;
        if (header != null) {
            readGroup = (String) record.getAttribute("RG");
            if (readGroup != null) {
                SAMReadGroupRecord rgRec = header.getReadGroup(readGroup);
                if (rgRec != null) {
                    this.sample = rgRec.getSample();
                    this.library = rgRec.getLibrary();
                    flowOrder = rgRec.getFlowOrder();
                    keySequence = rgRec.getKeySequence();
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        }
        return header;
    }

    public List<String> getSequenceNames() {
        SAMFileHeader header = getFileHeader();
        if (header == null) {
            return null;
        }
        List<String> seqNames = new ArrayList();
        List<SAMSequenceRecord> records = header.getSequenceDictionary().getSequences();
        if (records.size() > 0) {
            for (SAMSequenceRecord rec : header.getSequenceDictionary().getSequences()) {
                String chr = rec.getSequenceName();
                seqNames.add(chr);
            }
        }
        return seqNames;
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        reader = null;
    }

    @Test
    public void testGetHeader() throws IOException {
        SAMFileHeader header = reader.getFileHeader();
        assertEquals(114, header.getSequenceDictionary().size());
        assertEquals("1.0", header.getVersion());
    }
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            sampleRGs.add(rg);
            sample2RG.put(sample, rg);
        }

        // initialize BAM headers
        header = new SAMFileHeader();
        header.setSequenceDictionary(getToolkit().getReferenceDataSource().getReference().getSequenceDictionary());
        header.setSortOrder(SAMFileHeader.SortOrder.coordinate);
        header.setReadGroups(sampleRGs);

        final SAMProgramRecord programRecord = new SAMProgramRecord(PROGRAM_RECORD_NAME);
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        return ArtificialSAMUtils.createArtificialSamHeader(artificialSAMSequenceDictionary());
    }

    public List<GATKSAMRecord> readList() {
        if (readList == null) {
            final SAMFileHeader header = artificialSAMFileHeader();
            readList = new ArrayList<>(readCigars.length);
            final List<String> haplotypes = haplotypesStrings();
            int count = 0;
            for (final String descr : readCigars) {
                String sequence;
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    }

    protected ReadDestination(final SAMFileHeader header, final String readGroupID) {
        // prepare the bam header
        if ( header == null ) throw new IllegalArgumentException("header cannot be null");
        bamHeader = new SAMFileHeader();
        bamHeader.setSequenceDictionary(header.getSequenceDictionary());
        bamHeader.setSortOrder(SAMFileHeader.SortOrder.coordinate);

        // include the original read groups plus a new artificial one for the haplotypes
        final List<SAMReadGroupRecord> readGroups = new ArrayList<SAMReadGroupRecord>(header.getReadGroups());
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     *
     * @param originalHeader      original header
     * @param programRecord       the program record for this program
     */
    public static SAMFileHeader setupWriter(final SAMFileHeader originalHeader, final SAMProgramRecord programRecord) {
        final SAMFileHeader header = originalHeader.clone();
        final List<SAMProgramRecord> oldRecords = header.getProgramRecords();
        final List<SAMProgramRecord> newRecords = new ArrayList<SAMProgramRecord>(oldRecords.size()+1);
        for ( SAMProgramRecord record : oldRecords )
            if ( (programRecord != null && !record.getId().startsWith(programRecord.getId())))
                newRecords.add(record);

        if (programRecord != null) {
            newRecords.add(programRecord);
            header.setProgramRecords(newRecords);
        }
        return header;
    }
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Related Classes of htsjdk.samtools.SAMFileHeader

  • org.broad.igv.sam.PicardAlignment
  • org.broad.igv.sam.reader.BAMFileReader
  • org.broad.igv.sam.reader.BAMHttpQueryReaderTest
  • org.broad.igv.sam.reader.BAMHttpReader
  • org.broad.igv.sam.reader.MergedAlignmentReader
  • org.broad.igv.sam.reader.SAMFileGroup
  • org.broadinstitute.gatk.engine.datasources.reads.ActiveRegionShardBalancerUnitTest
  • org.broadinstitute.gatk.engine.downsampling.AlleleBiasedDownsamplingUtilsUnitTest
  • org.broadinstitute.gatk.engine.downsampling.DownsamplingReadsIteratorUnitTest
  • org.broadinstitute.gatk.engine.downsampling.FractionalDownsamplerUnitTest$FractionalDownsamplerTest
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