/** Create a ReadDestination that writes to a BAM file */
public ToBAM(
final StingSAMFileWriter stingSAMWriter,
final SAMFileHeader header,
final String readGroupID) {
super(header, readGroupID);
if (stingSAMWriter == null) throw new IllegalArgumentException("writer cannot be null");
bamWriter = stingSAMWriter;
stingSAMWriter.setPresorted(false);
stingSAMWriter.writeHeader(getHeader());
}
/**
* Creates a program record for the program, adds it to the list of program records (@PG tags) in
* the bam file and sets up the writer with the header and presorted status.
*
* @param writer BAM file writer
* @param toolkit the engine
* @param preSorted whether or not the writer can assume reads are going to be added are already
* sorted
* @param KEEP_ALL_PG_RECORDS whether or not to keep all the other program records already
* existing in this BAM file
* @param walker the walker object (so we can extract the command line)
* @param PROGRAM_RECORD_NAME the name for the PG tag
*/
public static void setupWriter(
StingSAMFileWriter writer,
GenomeAnalysisEngine toolkit,
SAMFileHeader originalHeader,
boolean preSorted,
boolean KEEP_ALL_PG_RECORDS,
Object walker,
String PROGRAM_RECORD_NAME) {
SAMFileHeader header =
setupWriter(toolkit, originalHeader, KEEP_ALL_PG_RECORDS, walker, PROGRAM_RECORD_NAME);
writer.writeHeader(header);
writer.setPresorted(preSorted);
}