protected int createSupplementaryAlignmentFastq(File input, File fq, boolean isRecursive) throws IOException {
int recordsWritten = 0;
try (SamReader reader = readerFactory.open(input)) {
try (AsyncBufferedIterator<SAMRecord> bufferedIt = new AsyncBufferedIterator<>(reader.iterator(), input.getName())) {
try (FastqWriter writer = new AsyncFastqWriter(new NonFlushingBasicFastqWriter(fq), AsyncFastqWriter.DEFAULT_QUEUE_SIZE)) {
SplitReadFastqExtractionIterator fastqit = new SplitReadFastqExtractionIterator(
bufferedIt,
isRecursive,
minSoftClipLength,
minSoftClipQuality,
!isRecursive && isProcessSecondaryAlignments(),
isRealignExistingSplitReads(),
isRealignEntireRecord(),
eidgen);
while (fastqit.hasNext()) {
writer.write(fastqit.next());
recordsWritten++;
}
}
}
}
return recordsWritten;
}
public boolean isRealignExistingSplitReads() {