Java Code Examples for htsjdk.samtools.SAMFileHeader#getSequence()
The following examples show how to use
htsjdk.samtools.SAMFileHeader#getSequence() .
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Example 1
Source File: CreateIntervalsFiles.java From Drop-seq with MIT License | 5 votes |
/** * Create a SAM header with a subset of the sequences * @param samHeader header to be subsetted * @param sequenceNames sequences to include * @return clone of the original header, but with only the named sequences */ private static SAMFileHeader createSubsetSamHeader(final SAMFileHeader samHeader, final List<String> sequenceNames) { final SAMFileHeader ret = samHeader.clone(); final List<SAMSequenceRecord> sequenceRecords = new ArrayList<>(sequenceNames.size()); for (final String sequence: sequenceNames) { final SAMSequenceRecord sequenceRecord = ret.getSequence(sequence); if (sequenceRecord == null) throw new RuntimeException("Sequence '" + sequence + "' specified on command line but not found in sequence dictionary"); sequenceRecords.add(sequenceRecord); } ret.getSequenceDictionary().setSequences(sequenceRecords); return ret; }
Example 2
Source File: HeaderInfo.java From dataflow-java with Apache License 2.0 | 5 votes |
public static HeaderInfo getHeaderFromBAMFile(Storage.Objects storage, String BAMPath, Iterable<Contig> explicitlyRequestedContigs) throws IOException { HeaderInfo result = null; // Open and read start of BAM LOG.info("Reading header from " + BAMPath); final SamReader samReader = BAMIO .openBAM(storage, BAMPath, ValidationStringency.DEFAULT_STRINGENCY); final SAMFileHeader header = samReader.getFileHeader(); Contig firstContig = getFirstExplicitContigOrNull(header, explicitlyRequestedContigs); if (firstContig == null) { final SAMSequenceRecord seqRecord = header.getSequence(0); firstContig = new Contig(seqRecord.getSequenceName(), -1, -1); } LOG.info("Reading first chunk of reads from " + BAMPath); final SAMRecordIterator recordIterator = samReader.query( firstContig.referenceName, (int)firstContig.start + 1, (int)firstContig.end + 1, false); Contig firstShard = null; while (recordIterator.hasNext() && result == null) { SAMRecord record = recordIterator.next(); final int alignmentStart = record.getAlignmentStart(); if (firstShard == null && alignmentStart > firstContig.start && (alignmentStart < firstContig.end || firstContig.end == -1)) { firstShard = new Contig(firstContig.referenceName, alignmentStart, alignmentStart); LOG.info("Determined first shard to be " + firstShard); result = new HeaderInfo(header, firstShard); } } recordIterator.close(); samReader.close(); if (result == null) { throw new IOException("Did not find reads for the first contig " + firstContig.toString()); } LOG.info("Finished header reading from " + BAMPath); return result; }
Example 3
Source File: PSBwaUtils.java From gatk with BSD 3-Clause "New" or "Revised" License | 5 votes |
static void addReferenceSequencesToHeader(final SAMFileHeader header, final String referenceDictionaryPath) { final List<SAMSequenceRecord> refSeqs = getReferenceSequences(referenceDictionaryPath); for (final SAMSequenceRecord rec : refSeqs) { if (header.getSequence(rec.getSequenceName()) == null) { header.addSequence(rec); } } }
Example 4
Source File: SAMFileHeader_Utils.java From cramtools with Apache License 2.0 | 4 votes |
static SAMFileHeader readHeader(final BinaryCodec stream, final ValidationStringency validationStringency, final String source) throws IOException { final byte[] buffer = new byte[4]; stream.readBytes(buffer); if (!Arrays.equals(buffer, "BAM\1".getBytes())) { throw new IOException("Invalid BAM file header"); } final int headerTextLength = stream.readInt(); final String textHeader = stream.readString(headerTextLength); final SAMTextHeaderCodec headerCodec = new SAMTextHeaderCodec(); headerCodec.setValidationStringency(validationStringency); final SAMFileHeader samFileHeader = headerCodec.decode(new StringLineReader(textHeader), source); final int sequenceCount = stream.readInt(); if (samFileHeader.getSequenceDictionary().size() > 0) { // It is allowed to have binary sequences but no text sequences, so // only validate if both are present if (sequenceCount != samFileHeader.getSequenceDictionary().size()) { throw new SAMFormatException("Number of sequences in text header (" + samFileHeader.getSequenceDictionary().size() + ") != number of sequences in binary header (" + sequenceCount + ") for file " + source); } for (int i = 0; i < sequenceCount; i++) { final SAMSequenceRecord binarySequenceRecord = readSequenceRecord(stream, source); final SAMSequenceRecord sequenceRecord = samFileHeader.getSequence(i); if (!sequenceRecord.getSequenceName().equals(binarySequenceRecord.getSequenceName())) { throw new SAMFormatException("For sequence " + i + ", text and binary have different names in file " + source); } if (sequenceRecord.getSequenceLength() != binarySequenceRecord.getSequenceLength()) { throw new SAMFormatException("For sequence " + i + ", text and binary have different lengths in file " + source); } } } else { // If only binary sequences are present, copy them into // samFileHeader final List<SAMSequenceRecord> sequences = new ArrayList<SAMSequenceRecord>(sequenceCount); for (int i = 0; i < sequenceCount; i++) { sequences.add(readSequenceRecord(stream, source)); } samFileHeader.setSequenceDictionary(new SAMSequenceDictionary(sequences)); } return samFileHeader; }