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@CommandLineProgramProperties(summary = "Create a Hadoop BAM splitting index and optionally a BAM index from a BAM file",
oneLineSummary = "Create a Hadoop BAM splitting index" ,
programGroup = OtherProgramGroup.class)
@DocumentedFeature
@BetaFeature
public final class CreateHadoopBamSplittingIndex extends CommandLineProgram {
private static final Logger logger = LogManager.getLogger(CreateHadoopBamSplittingIndex.class);
public static final String SPLITTING_INDEX_GRANULARITY_LONG_NAME = "splitting-index-granularity";
public static final String CREATE_BAI_LONG_NAME = "create-bai";
@Argument(fullName = StandardArgumentDefinitions.INPUT_LONG_NAME,
shortName = StandardArgumentDefinitions.INPUT_SHORT_NAME,
doc = "BAM file to create a HadoopBam splitting index for",
optional = false )
public File inputBam;
@Argument(fullName = StandardArgumentDefinitions.READ_VALIDATION_STRINGENCY_LONG_NAME,
shortName = StandardArgumentDefinitions.READ_VALIDATION_STRINGENCY_SHORT_NAME,
doc = "Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default stringency value SILENT " +
"can improve performance when processing a BAM file in which variable-length data (read, qualities, tags) " +
"do not otherwise need to be decoded.",
common=true,
optional=true)
public ValidationStringency readValidationStringency = ReadConstants.DEFAULT_READ_VALIDATION_STRINGENCY;
@Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME,
shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME,
doc = "The splitting index (SBI) file. If this is unspecified an index will be created with the same name as " +
"the input file but with the additional extension " + FileExtensions.SBI,
optional = true)
public File output;
@Argument(fullName = SPLITTING_INDEX_GRANULARITY_LONG_NAME,
doc = "Splitting index granularity, an entry is created in the index every this many reads.",
optional = true)
public long granularity = SBIIndexWriter.DEFAULT_GRANULARITY;
@Argument(fullName = CREATE_BAI_LONG_NAME,
doc = "Set this to create a bai index at the same time as creating a splitting index",
optional = true)
public boolean createBai = false;
@Override
public Object doWork() {
if( granularity <= 0) {
throw new CommandLineException.BadArgumentValue(SPLITTING_INDEX_GRANULARITY_LONG_NAME, Long.toString(granularity), "Granularity must be > 0");
}
final File index = getOutputFile(output, inputBam);
if(createBai){
createBaiAndSplittingIndex(inputBam, index, granularity, readValidationStringency);
} else {
createOnlySplittingIndex(inputBam, index, granularity);
}
return 0;
}
private static void createOnlySplittingIndex(final File inputBam, final File index, final long granularity) {
assertIsBam(inputBam);
try(SeekableStream in = new SeekableFileStream(inputBam);
BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(index))) {
BAMSBIIndexer.createIndex(in, out, granularity);
} catch (final IOException e) {
throw new UserException("Couldn't create splitting index", e);
}
}
private static void createBaiAndSplittingIndex(final File inputBam, final File index, final long granularity, final ValidationStringency readValidationStringency) {
assertIsBam(inputBam);
try(SamReader reader = SamReaderFactory.makeDefault()
.validationStringency(readValidationStringency)
.setOption(SamReaderFactory.Option.INCLUDE_SOURCE_IN_RECORDS, true)
.open(inputBam);
BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(index))) {
final SAMFileHeader header = reader.getFileHeader();
assertBamIsCoordinateSorted(header);
final SBIIndexWriter indexer = new SBIIndexWriter(out, granularity);
final BAMIndexer bamIndexer = new BAMIndexer(IOUtils.replaceExtension(index, FileExtensions.BAI_INDEX), header);
BAMFileSpan lastFilePointer = null;
for(final SAMRecord read : reader){
BAMFileSpan filePointer = (BAMFileSpan) read.getFileSource().getFilePointer();
indexer.processRecord(filePointer.getFirstOffset());
bamIndexer.processAlignment(read);
lastFilePointer = filePointer;
}
long nextStart = 0;
if (lastFilePointer != null && !lastFilePointer.getChunks().isEmpty()) {
nextStart = lastFilePointer.getChunks().get(0).getChunkEnd();
}
if (nextStart == 0) {
nextStart = BlockCompressedFilePointerUtil.makeFilePointer(inputBam.length()); // default to file length (in case of no reads)
}
indexer.finish(nextStart, inputBam.length()); // nextStart is start of next record that would be added
bamIndexer.finish();
} catch (final IOException e) {
throw new UserException("Couldn't create splitting index", e);
}
}
private static void assertBamIsCoordinateSorted(final SAMFileHeader header) {
if( header.getSortOrder() != SAMFileHeader.SortOrder.coordinate) {
throw new UserException.BadInput("Cannot create a " + FileExtensions.BAI_INDEX + " index for a file " +
"that isn't coordinate sorted.");
}
}
private static void assertIsBam(final File inputBam) {
if(!BamFileIoUtils.isBamFile(inputBam)) {
throw new UserException.BadInput("A splitting index is only relevant for a bam file, but a "
+ "file with extension "+ FileUtils.getExtension(inputBam.getName()) + " was specified.");
}
}
private static File getOutputFile(final File suggestedOutput, final File input) {
if(suggestedOutput == null){
return new File(input.getPath() + FileExtensions.SBI);
} else {
if (!suggestedOutput.getAbsolutePath().endsWith("bam" + FileExtensions.SBI)){
logger.warn("Creating a splitting index (SBI) with an extension that doesn't match "
+ "bam"+ FileExtensions.SBI + ". Output file: "+suggestedOutput);
}
return suggestedOutput;
}
}
}
