public CRAMFileWriter makeCRAMWriter(
final SAMFileHeader header, final File outputFile, final File referenceFasta) {
final boolean createIndex = this.createIndex && IOUtil.isRegularPath(outputFile);
if (this.createIndex && !createIndex) {
System.err.println(
"Cannot create index for CAM because output file is not a regular file: "
+ outputFile.getAbsolutePath());
}
try {
OutputStream indexOS = null;
if (createIndex) {
File indexFile = new File(outputFile.getAbsolutePath() + ".bai");
indexOS = new FileOutputStream(indexFile);
}
final CRAMFileWriter writer =
new CRAMFileWriter(
new FileOutputStream(outputFile),
indexOS,
new ReferenceSource(referenceFasta),
header,
null);
writer.setPreserveReadNames(true);
writer.setCaptureAllTags(true);
return writer;
} catch (final IOException ioe) {
throw new RuntimeIOException("Error opening file: " + outputFile.getAbsolutePath());
}
}
public CRAMFileWriter makeCRAMWriter(
final SAMFileHeader header, final OutputStream stream, final File referenceFasta) {
final CRAMFileWriter writer =
new CRAMFileWriter(stream, new ReferenceSource(referenceFasta), header, null);
writer.setPreserveReadNames(true);
writer.setCaptureAllTags(true);
return writer;
}