/**
* Generates a BAM index file from an input BAM file
*
* @param reader SAMFileReader for input BAM file
* @param output File for output index file
*/
public static void createIndex(SAMFileReader reader, File output, Log log) {
BAMIndexer indexer = new BAMIndexer(output, reader.getFileHeader());
reader.enableFileSource(true);
int totalRecords = 0;
// create and write the content
for (SAMRecord rec : reader) {
if (++totalRecords % 1000000 == 0) {
if (null != log) log.info(totalRecords + " reads processed ...");
}
indexer.processAlignment(rec);
}
indexer.finish();
}