/**
* Concatenate VCF files of non-overlapping genome intervals, all with the same set of samples
*
* <p>The main purpose of this tool is to speed up the gather function when using scatter-gather
* parallelization. This tool concatenates the scattered output VCF files. It assumes that:
*
* <ul>
* <li>All the input VCFs (or BCFs) contain the same samples in the same order.
* <li>The variants in each input file are from non-overlapping (scattered) intervals.
* </ul>
*
* <p>When the input files are already sorted based on the intervals start positions, use
* -assumeSorted.
*
* <h3>Input</h3>
*
* <p>Two or more variant sets to combine. They should be of non-overlapping genome intervals and
* with the same samples (sorted in the same order). If the files are ordered according to the
* appearance of intervals in the ref genome, then one can use the -assumeSorted flag.
*
* <h3>Output</h3>
*
* <p>A combined VCF or BCF. The output file should have the same extension as the input(s). <\p>
*
* <h3>Important note</h3>
*
* <p>This is a command-line utility that bypasses the GATK engine. As a result, the command-line
* you must use to invoke it is a little different from other GATK tools (see example below), and it
* does not accept any of the classic "CommandLineGATK" arguments.
*
* <h3>Usage example</h3>
*
* <pre>
* java -cp GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants \
* -R reference.fasta \
* -V input1.vcf \
* -V input2.vcf \
* -out output.vcf \
* -assumeSorted
* </pre>
*
* <h3>Caveat</h3>
*
* <p>Currently the tool is more efficient when working with VCFs than with BCFs.
*
* @author Ami Levy Moonshine
* @since Jan 2012
*/
@DocumentedGATKFeature(groupName = HelpConstants.DOCS_CAT_VARMANIP)
public class CatVariants extends CommandLineProgram {
// setup the logging system, used by some codecs
private static org.apache.log4j.Logger logger = org.apache.log4j.Logger.getRootLogger();
@Input(
fullName = "reference",
shortName = "R",
doc = "genome reference file <name>.fasta",
required = true)
private File refFile = null;
/**
* The VCF or BCF files to merge together
*
* <p>CatVariants can take any number of -V arguments on the command line. Each -V argument will
* be included in the final merged output VCF/BCF. The order of arguments does not matter, but it
* runs more efficiently if they are sorted based on the intervals and the assumeSorted argument
* is used.
*/
@Input(fullName = "variant", shortName = "V", doc = "Input VCF file/s", required = true)
private List<File> variant = null;
@Output(fullName = "outputFile", shortName = "out", doc = "output file", required = true)
private File outputFile = null;
@Argument(
fullName = "assumeSorted",
shortName = "assumeSorted",
doc =
"assumeSorted should be true if the input files are already sorted (based on the position of the variants)",
required = false)
private Boolean assumeSorted = false;
@Argument(
fullName = "variant_index_type",
doc = "which type of IndexCreator to use for VCF/BCF indices",
required = false)
private GATKVCFIndexType variant_index_type = GATKVCFUtils.DEFAULT_INDEX_TYPE;
@Argument(
fullName = "variant_index_parameter",
doc = "the parameter (bin width or features per bin) to pass to the VCF/BCF IndexCreator",
required = false)
private Integer variant_index_parameter = GATKVCFUtils.DEFAULT_INDEX_PARAMETER;
/*
* print usage information
*/
private static void printUsage() {
System.err.println(
"Usage: java -cp target/GenomeAnalysisTK.jar org.broadinstitute.gatk.tools.CatVariants --reference <reference> --variant <input VCF or BCF file; can specify --variant multiple times> --outputFile <outputFile> [--assumeSorted]");
System.err.println(" The output file must be of the same type as all input files.");
System.err.println(
" If the input files are already sorted, then indicate that with --assumeSorted to improve performance.");
}
private enum FileType {
VCF,
BCF,
BLOCK_COMPRESSED_VCF,
INVALID
}
private FileType fileExtensionCheck(File inFile, FileType previousFileType) {
final String inFileName = inFile.toString().toLowerCase();
if (inFileName.endsWith(".vcf")) {
if (previousFileType == FileType.VCF || previousFileType == null) {
return FileType.VCF;
}
}
if (inFileName.endsWith(".bcf")) {
if (previousFileType == FileType.BCF || previousFileType == null) {
return FileType.BCF;
}
}
for (String extension : AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS) {
if (inFileName.endsWith(".vcf" + extension)) {
if (previousFileType == FileType.BLOCK_COMPRESSED_VCF || previousFileType == null) {
return FileType.BLOCK_COMPRESSED_VCF;
}
}
}
System.err.println(
String.format("File extension for input file %s is not valid for CatVariants", inFile));
printUsage();
return FileType.INVALID;
}
private FeatureReader<VariantContext> getFeatureReader(final FileType fileType, final File file) {
FeatureReader<VariantContext> reader = null;
switch (fileType) {
case VCF:
case BLOCK_COMPRESSED_VCF:
// getFeatureReader will handle both block-compressed and plain text VCFs
reader =
AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new VCFCodec(), false);
break;
case BCF:
reader =
AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new BCF2Codec(), false);
break;
}
return reader;
}
/**
* Replaces any .list files in rawFileList with the files named in said .list file
*
* @param rawFileList the original file list, possibly including .list files
* @return a new List, with .list files replaced
*/
private List<File> parseVariantList(final List<File> rawFileList) {
final List<File> result = new ArrayList<>(rawFileList.size());
for (final File rawFile : rawFileList) {
if (rawFile.getName().endsWith(".list")) {
try {
for (final String line : new XReadLines(rawFile, true)) result.add(new File(line));
} catch (IOException e) {
throw new UserException.CouldNotReadInputFile(rawFile, e);
}
} else {
result.add(rawFile);
}
}
return result;
}
@Override
protected int execute() throws Exception {
BasicConfigurator.configure();
logger.setLevel(Level.INFO);
final ReferenceSequenceFile ref;
try {
ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(refFile);
} catch (Exception e) {
throw new UserException("Couldn't load provided reference sequence file " + refFile, e);
}
variant = parseVariantList(variant);
Comparator<Pair<Integer, File>> positionComparator = new PositionComparator();
Queue<Pair<Integer, File>> priorityQueue;
if (assumeSorted) priorityQueue = new LinkedList<>();
else priorityQueue = new PriorityQueue<>(10000, positionComparator);
FileType fileType = null;
for (File file : variant) {
// if it returns a valid type, it will be the same for all files
fileType = fileExtensionCheck(file, fileType);
if (fileType == FileType.INVALID) return 1;
if (assumeSorted) {
priorityQueue.add(new Pair<>(0, file));
} else {
if (!file.exists()) {
throw new UserException(String.format("File %s doesn't exist", file.getAbsolutePath()));
}
FeatureReader<VariantContext> reader = getFeatureReader(fileType, file);
Iterator<VariantContext> it = reader.iterator();
if (!it.hasNext()) {
System.err.println(
String.format("File %s is empty. This file will be ignored", file.getAbsolutePath()));
continue;
}
VariantContext vc = it.next();
int firstPosition = vc.getStart();
reader.close();
priorityQueue.add(new Pair<>(firstPosition, file));
}
}
FileOutputStream outputStream = new FileOutputStream(outputFile);
EnumSet<Options> options = EnumSet.of(Options.INDEX_ON_THE_FLY);
IndexCreator idxCreator =
GATKVCFUtils.makeIndexCreator(
variant_index_type, variant_index_parameter, outputFile, ref.getSequenceDictionary());
final VariantContextWriter outputWriter =
VariantContextWriterFactory.create(
outputFile, outputStream, ref.getSequenceDictionary(), idxCreator, options);
boolean firstFile = true;
int count = 0;
while (!priorityQueue.isEmpty()) {
count++;
File file = priorityQueue.remove().getSecond();
if (!file.exists()) {
throw new UserException(String.format("File %s doesn't exist", file.getAbsolutePath()));
}
FeatureReader<VariantContext> reader = getFeatureReader(fileType, file);
if (count % 10 == 0) System.out.print(count);
else System.out.print(".");
if (firstFile) {
VCFHeader header = (VCFHeader) reader.getHeader();
outputWriter.writeHeader(header);
firstFile = false;
}
Iterator<VariantContext> it = reader.iterator();
while (it.hasNext()) {
VariantContext vc = it.next();
outputWriter.add(vc);
}
reader.close();
}
System.out.println();
outputWriter.close();
return 0;
}
public static void main(String[] args) {
try {
CatVariants instance = new CatVariants();
start(instance, args);
System.exit(CommandLineProgram.result);
} catch (UserException e) {
printUsage();
exitSystemWithUserError(e);
} catch (Exception e) {
exitSystemWithError(e);
}
}
private static class PositionComparator implements Comparator<Pair<Integer, File>> {
@Override
public int compare(Pair<Integer, File> p1, Pair<Integer, File> p2) {
int startPositionP1 = p1.getFirst();
int startPositionP2 = p2.getFirst();
if (startPositionP1 == startPositionP2) return 0;
return startPositionP1 < startPositionP2 ? -1 : 1;
}
}
}
