@Override public void setInputStream(final InputStream is) { bamCodec.setInputStream(is); }
@Override public void setInputStream(final InputStream is) { bamCodec.setInputStream(is); }
@Override public void readFields(DataInput in) throws IOException { lazyCodec.setInputStream(new DataInputWrapper(in)); record = lazyCodec.decode(); }
@Override public void readFields(DataInput in) throws IOException { lazyCodec.setInputStream(new DataInputWrapper(in)); record = lazyCodec.decode(); }
@Override public void readFields(DataInput in) throws IOException { lazyCodec.setInputStream(new DataInputWrapper(in)); record = lazyCodec.decode(); }
private List<SAMRecord> toSAMRecord(BAMRecordView view, SAMFileHeader samHeader) { BAMRecordCodec bc = new BAMRecordCodec(samHeader); bc.setInputStream(new ByteArrayInputStream(view.buf, 0, view.start)); List<SAMRecord> records = new ArrayList<SAMRecord>(); SAMRecord record; while ((record = bc.decode()) != null) { records.add(record); } return records; }
throw new IllegalArgumentException(); codec.setInputStream(new ByteArrayInputStream(object.bytes)); SAMRecord samRecord = null; List<SAMRecord> records = new ArrayList<SAMRecord>();
/** * @param advance Trick to enable subclass to do more setup before advancing */ BAMFileIterator(final boolean advance) { this.bamRecordCodec = new BAMRecordCodec(getFileHeader(), samRecordFactory); this.bamRecordCodec.setInputStream(BAMFileReader.this.mStream.getInputStream(), BAMFileReader.this.mStream.getInputFileName()); if (advance) { advance(); } }
/** * @param advance Trick to enable subclass to do more setup before advancing */ BAMFileIterator(final boolean advance) { this.bamRecordCodec = new BAMRecordCodec(getFileHeader(), samRecordFactory); this.bamRecordCodec.setInputStream(BAMFileReader.this.mStream.getInputStream(), BAMFileReader.this.mStream.getInputFileName()); if (advance) { advance(); } }
/** * @param advance Trick to enable subclass to do more setup before advancing */ BAMFileIterator(final boolean advance) { this.bamRecordCodec = new BAMRecordCodec(getFileHeader(), samRecordFactory); this.bamRecordCodec.setInputStream(BAMFileReader.this.mStream.getInputStream(), BAMFileReader.this.mStream.getInputFileName()); if (advance) { advance(); } }
/** * @param advance Trick to enable subclass to do more setup before advancing */ BAMFileIterator(final boolean advance) { this.bamRecordCodec = new BAMRecordCodec(getFileHeader(), samRecordFactory); this.bamRecordCodec.setInputStream(BAMFileReader.this.mStream.getInputStream(), BAMFileReader.this.mStream.getInputFileName()); if (useAsynchronousIO) { mAsync = new AsyncBamDecoder(ASYNC_BATCH_SIZE_IN_BYTES, Defaults.NON_ZERO_BUFFER_SIZE); mAvailableIdleCodec = new ConcurrentLinkedQueue<>(); } else { mAsync = null; mAvailableIdleCodec = null; } if (advance) { advance(); } }
private List<SAMRecord> getRecordsAtSplits(File bam, SplittingBAMIndex index) throws IOException { List<SAMRecord> records = new ArrayList<>(); BAMRecordCodec codec = new BAMRecordCodec(samFileHeader); BlockCompressedInputStream bci = new BlockCompressedInputStream(bam); codec.setInputStream(bci); for (Long offset : index.getVirtualOffsets()) { bci.seek(offset); SAMRecord record = codec.decode(); if (record != null) { records.add(record); } } return records; }
codec.setInputStream(is); } else { codec.setInputStream(is, mStream.getInputFileName());
inputStream.submitAccessPlan(new BAMAccessPlan(id, inputStream, (GATKBAMFileSpan) shard.getFileSpans().get(id))); BAMRecordCodec codec = new BAMRecordCodec(getHeader(id)); codec.setInputStream(inputStream); iterator = new BAMCodecIterator(inputStream,readers.getReader(id),codec);
bc.setInputStream(new ByteArrayInputStream(view.buf)); SAMRecord record = bc.decode(); assertThat(record.getReadName(), is("readName"));
this.bgzf.setCheckCrcs(true); this.bamCodec.setInputStream(bgzf);
this.bgzf.setCheckCrcs(true); this.bamCodec.setInputStream(bgzf);