/** * @{inheritDoc} */ public void close() { dest.close(); }
@Override public void close() { writer.close(); } }
@Override public void close() { writer.close(); } }
@Override public boolean close() { writer.close(); return true; }
/** * Close down this reference model, closing down any debugging information opened during execution */ public void close() { if ( debuggingWriter != null ) debuggingWriter.close(); }
protected void closeWriter() { out.close(); }
@Override public void onTraversalDone(Map<String, SAMFileWriter> outputs) { for ( SAMFileWriter output : outputs.values() ) { output.close(); } }
void close() { if (outputByReadGroup) { writerMap.values().forEach(SAMFileWriter::close); } else { singleWriter.close(); } } }
void close() { if (outputByReadGroup) { writerMap.values().forEach(SAMFileWriter::close); } else { singleWriter.close(); } } }
/** Closes the underlying resource. */ void close() { if (this.writer != null) { this.writer.close(); } if (this.sorter != null) { this.sorter.doneAdding(); } } }
/** Closes the underlying resource. */ void close() { if (this.writer != null) { this.writer.close(); } if (this.sorter != null) { this.sorter.doneAdding(); } } }
/** * @{inheritDoc} */ public void close() { outputTracker.getStorage(this).close(); }
@Override public void finish() { for (FastqRead read : readSet.keySet()) kickedFromCache(read); readSet.clear(); if (writer != null) writer.close(); writer = null; }
private int writeAlignments(SAMFileWriter writer, Iterator<PicardAlignment> alignments) { int count = 0; while (alignments.hasNext()) { PicardAlignment al = alignments.next(); writer.addAlignment(al.getRecord()); count++; } writer.close(); return count; }
@Override protected void finish() { writer.close(); if (tmpOut != OUTPUT) { try { FileHelper.move(tmpOut, OUTPUT, true); } catch (IOException e) { throw new RuntimeIOException(e); } } } }
public void close() { try { writer.close(); } catch (RuntimeIOException e) { throw new UserException.ErrorWritingBamFile(e.getMessage()); } }
/** * Write the reads from this builder to output, creating an index as well * @param output the output BAM file we want to use * @return */ public File makeBAMFile(final File output) { final SAMFileWriter writer = factory.makeBAMWriter(header, true, output, 0); for ( final GATKSAMRecord read : makeReads() ) writer.addAlignment(read); writer.close(); return output; }
private void createBAM(final List<GATKSAMRecord> reads) throws IOException { testBAM = createTempFile("TraverseActiveRegionsUnitTest", ".bam"); SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(reads.get(0).getHeader(), true, testBAM); for (GATKSAMRecord read : reads ) { out.addAlignment(read); } out.close(); new File(testBAM.getAbsolutePath().replace(".bam", ".bai")).deleteOnExit(); new File(testBAM.getAbsolutePath() + ".bai").deleteOnExit(); }
private void createBAM(List<GATKSAMRecord> reads) throws IOException { testBAM = createTempFile("TraverseActiveRegionsUnitTest", ".bam"); SAMFileWriter out = new SAMFileWriterFactory().setCreateIndex(true).makeBAMWriter(reads.get(0).getHeader(), true, testBAM); for (GATKSAMRecord read : ReadUtils.sortReadsByCoordinate(reads)) { out.addAlignment(read); } out.close(); new File(testBAM.getAbsolutePath().replace(".bam", ".bai")).deleteOnExit(); new File(testBAM.getAbsolutePath() + ".bai").deleteOnExit(); }
private File createInputFile() { // Create the input file final File input = new File(outputDir, "input.sam"); final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(samRecordSetBuilder.getHeader(), true, input); samRecordSetBuilder.getRecords().forEach(writer::addAlignment); writer.close(); return input; }