/**
* Generates a BAM index file, either textual or binary, from an input BAI file. Only used for
* testing, but located here for visibility into CachingBAMFileIndex.
*
* @param output BAM Index (.bai) file (or bai.txt file when text)
* @param textOutput Whether to create text output or binary
*/
public static void createAndWriteIndex(
final File input, final File output, final boolean textOutput) {
// content is from an existing bai file.
final CachingBAMFileIndex existingIndex = new CachingBAMFileIndex(input, null);
final int n_ref = existingIndex.getNumberOfReferences();
final BAMIndexWriter outputWriter;
if (textOutput) {
outputWriter = new TextualBAMIndexWriter(n_ref, output);
} else {
outputWriter = new BinaryBAMIndexWriter(n_ref, output);
}
// write the content one reference at a time
try {
for (int i = 0; i < n_ref; i++) {
outputWriter.writeReference(existingIndex.getQueryResults(i));
}
outputWriter.writeNoCoordinateRecordCount(existingIndex.getNoCoordinateCount());
outputWriter.close();
} catch (final Exception e) {
throw new SAMException("Exception creating BAM index", e);
}
}
/** write out any references between the currentReference and the nextReference */
private void advanceToReference(final int nextReference) {
while (currentReference < nextReference) {
final BAMIndexContent content = indexBuilder.processReference(currentReference);
outputWriter.writeReference(content);
currentReference++;
if (currentReference < numReferences) {
indexBuilder.startNewReference();
}
}
}
/**
* After all the alignment records have been processed, finish is called. Writes any final
* information and closes the output file.
*/
public void finish() {
// process any remaining references
advanceToReference(numReferences);
outputWriter.writeNoCoordinateRecordCount(indexBuilder.getNoCoordinateRecordCount());
outputWriter.close();
}