/**
* Create a BAMFileWriter that is ready to receive SAMRecords.
*
* @param header entire header. Sort order is determined by the sortOrder property of this arg.
* @param presorted if true, SAMRecords must be added to the SAMFileWriter in order that agrees
* with header.sortOrder.
* @param outputFile where to write the output.
* @param compressionLevel Override default compression level with the given value, between 0
* (fastest) and 9 (smallest).
*/
public SAMFileWriter makeBAMWriter(
final SAMFileHeader header,
final boolean presorted,
final File outputFile,
final int compressionLevel) {
try {
final boolean createMd5File = this.createMd5File && IOUtil.isRegularPath(outputFile);
if (this.createMd5File && !createMd5File) {
System.err.println(
"Cannot create MD5 file for BAM because output file is not a regular file: "
+ outputFile.getAbsolutePath());
}
OutputStream os =
IOUtil.maybeBufferOutputStream(new FileOutputStream(outputFile, false), bufferSize);
if (createMd5File)
os = new Md5CalculatingOutputStream(os, new File(outputFile.getAbsolutePath() + ".md5"));
final BAMFileWriter ret = new BAMFileWriter(os, outputFile, compressionLevel);
final boolean createIndex = this.createIndex && IOUtil.isRegularPath(outputFile);
if (this.createIndex && !createIndex) {
System.err.println(
"Cannot create index for BAM because output file is not a regular file: "
+ outputFile.getAbsolutePath());
}
if (this.tmpDir != null) ret.setTempDirectory(this.tmpDir);
initializeBAMWriter(ret, header, presorted, createIndex);
if (this.useAsyncIo) return new AsyncSAMFileWriter(ret, this.asyncOutputBufferSize);
else return ret;
} catch (final IOException ioe) {
throw new RuntimeIOException("Error opening file: " + outputFile.getAbsolutePath());
}
}
