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CatVariants now handles BCF and Block-Compressed VCF 

[Delivers #67461500]
This commit is contained in:
Joel Thibault 2014-04-09 16:38:11 -04:00
parent 4c74319578
commit 1ab50f4ba8
1 changed files with 78 additions and 55 deletions
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133
public/gatk-framework/src/main/java/org/broadinstitute/sting/tools/CatVariants.java
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@ -53,7 +53,6 @@ import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFact
import java.io.*; import java.io.*;
import java.util.*; import java.util.*;
/** /**
* *
* Concatenates VCF files of non-overlapped genome intervals, all with the same set of samples * Concatenates VCF files of non-overlapped genome intervals, all with the same set of samples
@ -73,13 +72,12 @@ import java.util.*;
* <h3>Input</h3> * <h3>Input</h3>
* <p> * <p>
* One or more variant sets to combine. They should be of non-overlapping genome intervals and with the same samples (in the same order). * One or more variant sets to combine. They should be of non-overlapping genome intervals and with the same samples (in the same order).
* The input files should be 'name.vcf' or 'name.VCF' or 'name.bcf' or 'name.BCF'.
* If the files are ordered according to the appearance of intervals in the ref genome, then one can use the -assumeSorted flag. * If the files are ordered according to the appearance of intervals in the ref genome, then one can use the -assumeSorted flag.
* </p> * </p>
* *
* <h3>Output</h3> * <h3>Output</h3>
* <p> * <p>
* A combined VCF. The output file should be 'name.vcf' or 'name.VCF'. * A combined VCF or BCF. The output file should have the same extension as the input(s).
* <\p> * <\p>
* *
* <h3>Important note</h3> * <h3>Important note</h3>
@ -113,17 +111,17 @@ public class CatVariants extends CommandLineProgram {
* The VCF or BCF files to merge together * The VCF or BCF files to merge together
* *
* CatVariants can take any number of -V arguments on the command line. Each -V argument * CatVariants can take any number of -V arguments on the command line. Each -V argument
* will be included in the final merged output VCF. The order of arguments does not matter, but it runs more * 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. * 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 named <name>.vcf or <name>.bcf", required = true) @Input(fullName="variant", shortName="V", doc="Input VCF file/s", required = true)
private List<File> variant = null; private List<File> variant = null;
@Output(fullName = "outputFile", shortName = "out", doc = "output file name <name>.vcf or <name>.bcf", required = true) @Output(fullName = "outputFile", shortName = "out", doc = "output file", required = true)
private File outputFile = null; private File outputFile = null;
@Argument(fullName = "assumeSorted", shortName = "assumeSorted", doc = "assumeSorted should be true if he input files are already sorted (based on the position of the variants", required = false) @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; private Boolean assumeSorted = false;
@Argument(fullName = "variant_index_type", doc = "which type of IndexCreator to use for VCF/BCF indices", required = false) @Argument(fullName = "variant_index_type", doc = "which type of IndexCreator to use for VCF/BCF indices", required = false)
@ -137,19 +135,69 @@ public class CatVariants extends CommandLineProgram {
*/ */
private static void printUsage() { private static void printUsage() {
System.err.println("Usage: java -cp target/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants --reference <reference> --variant <input VCF or BCF file; can specify --variant multiple times> --outputFile <outputFile> [--assumeSorted]"); System.err.println("Usage: java -cp target/GenomeAnalysisTK.jar org.broadinstitute.sting.tools.CatVariants --reference <reference> --variant <input VCF or BCF file; can specify --variant multiple times> --outputFile <outputFile> [--assumeSorted]");
System.err.println(" The input file(s) can be of type: VCF (must end in .vcf or .VCF) or"); System.err.println(" The output file must be of the same type as all input files.");
System.err.println(" BCF2 (must end in .bcf or .BCF).");
System.err.println(" Output file must be of type vcf or bcf (must end in .vcf or .bcf).");
System.err.println(" If the input files are already sorted, then indicate that with --assumeSorted to improve performance."); 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, File outFile) {
final String inFileName = inFile.toString().toLowerCase();
final String outFileName = outFile.toString().toLowerCase();
FileType inFileType = FileType.INVALID;
if (inFileName.endsWith(".vcf")) {
inFileType = FileType.VCF;
if (outFileName.endsWith(".vcf"))
return inFileType;
}
if (inFileName.endsWith(".bcf")) {
inFileType = FileType.BCF;
if (outFileName.endsWith(".bcf"))
return inFileType;
}
for (String extension : AbstractFeatureReader.BLOCK_COMPRESSED_EXTENSIONS) {
if (inFileName.endsWith(".vcf" + extension)) {
inFileType = FileType.BLOCK_COMPRESSED_VCF;
if (outFileName.endsWith(".vcf" + extension))
return inFileType;
}
}
if (inFileType == FileType.INVALID)
System.err.println(String.format("File extension for input file %s is not valid for CatVariants", inFile));
else
System.err.println(String.format("File extension mismatch between input %s and output %s", inFile, outFile));
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;
}
@Override @Override
protected int execute() throws Exception { protected int execute() throws Exception {
//if(help){
// printUsage();
// return 1;
//}
BasicConfigurator.configure(); BasicConfigurator.configure();
logger.setLevel(Level.INFO); logger.setLevel(Level.INFO);
@ -162,37 +210,27 @@ public class CatVariants extends CommandLineProgram {
Comparator<Pair<Integer,File>> positionComparator = new PositionComparator(); Comparator<Pair<Integer,File>> positionComparator = new PositionComparator();
//PriorityQueue<Pair<Integer,FeatureReader<VariantContext>>> queue =
// new PriorityQueue<Pair<Integer,FeatureReader<VariantContext>>>(2000, comparator);
Queue<Pair<Integer,File>> priorityQueue; Queue<Pair<Integer,File>> priorityQueue;
if(assumeSorted) if (assumeSorted)
priorityQueue = new LinkedList<Pair<Integer,File>>(); priorityQueue = new LinkedList<>();
else else
priorityQueue = new PriorityQueue<Pair<Integer,File>>(10000, positionComparator); priorityQueue = new PriorityQueue<>(10000, positionComparator);
Iterator<File> files = variant.iterator(); FileType fileType = FileType.INVALID;
File file; for (File file : variant) {
while (files.hasNext()) { // if it returns a valid type, it will be the same for all files
file = files.next(); fileType = fileExtensionCheck(file, outputFile);
if (!(file.getName().endsWith(".vcf") || file.getName().endsWith(".VCF") || file.getName().endsWith(".bcf") || file.getName().endsWith(".BCF"))){ if (fileType == FileType.INVALID)
System.err.println("File " + file.getAbsolutePath() + " should be <name>.vcf or <name>.bcf");
printUsage();
return 1; return 1;
}
if (assumeSorted){ if (assumeSorted){
priorityQueue.add(new Pair<Integer, File>(0,file)); priorityQueue.add(new Pair<>(0,file));
} }
else{ else{
if (!file.exists()) { if (!file.exists()) {
throw new UserException(String.format("File %s doesn't exist",file.getAbsolutePath())); throw new UserException(String.format("File %s doesn't exist",file.getAbsolutePath()));
} }
FeatureReader<VariantContext> reader; FeatureReader<VariantContext> reader = getFeatureReader(fileType, file);
boolean useVCF = (file.getName().endsWith(".vcf") || file.getName().endsWith(".VCF"));
if(useVCF)
reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new VCFCodec(), false);
else
reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new BCF2Codec(), false);
Iterator<VariantContext> it = reader.iterator(); Iterator<VariantContext> it = reader.iterator();
if(!it.hasNext()){ if(!it.hasNext()){
System.err.println(String.format("File %s is empty. This file will be ignored",file.getAbsolutePath())); System.err.println(String.format("File %s is empty. This file will be ignored",file.getAbsolutePath()));
@ -201,37 +239,25 @@ public class CatVariants extends CommandLineProgram {
VariantContext vc = it.next(); VariantContext vc = it.next();
int firstPosition = vc.getStart(); int firstPosition = vc.getStart();
reader.close(); reader.close();
//queue.add(new Pair<Integer, FeatureReader<VariantContext>>(firstPosition,reader)); priorityQueue.add(new Pair<>(firstPosition,file));
priorityQueue.add(new Pair<Integer, File>(firstPosition,file));
} }
} }
if (!(outputFile.getName().endsWith(".vcf") || outputFile.getName().endsWith(".VCF"))){
throw new UserException(String.format("Output file %s should be <name>.vcf", outputFile));
}
FileOutputStream outputStream = new FileOutputStream(outputFile); FileOutputStream outputStream = new FileOutputStream(outputFile);
EnumSet<Options> options = EnumSet.of(Options.INDEX_ON_THE_FLY); EnumSet<Options> options = EnumSet.of(Options.INDEX_ON_THE_FLY);
final IndexCreator idxCreator = GATKVCFUtils.getIndexCreator(variant_index_type, variant_index_parameter, outputFile, ref.getSequenceDictionary()); final IndexCreator idxCreator = GATKVCFUtils.getIndexCreator(variant_index_type, variant_index_parameter, outputFile, ref.getSequenceDictionary());
final VariantContextWriter outputWriter = VariantContextWriterFactory.create(outputFile, outputStream, ref.getSequenceDictionary(), idxCreator, options); final VariantContextWriter outputWriter = VariantContextWriterFactory.create(outputFile, outputStream, ref.getSequenceDictionary(), idxCreator, options);
boolean firstFile = true; boolean firstFile = true;
int count =0; int count = 0;
//while(!queue.isEmpty()){
while(!priorityQueue.isEmpty() ){ while(!priorityQueue.isEmpty() ){
count++; count++;
//FeatureReader<VariantContext> reader = queue.remove().getSecond(); File file = priorityQueue.remove().getSecond();
file = priorityQueue.remove().getSecond();
if (!file.exists()) { if (!file.exists()) {
throw new UserException(String.format("File %s doesn't exist",file.getAbsolutePath())); throw new UserException(String.format("File %s doesn't exist",file.getAbsolutePath()));
} }
FeatureReader<VariantContext> reader; FeatureReader<VariantContext> reader = getFeatureReader(fileType, file);
boolean useVCF = (file.getName().endsWith(".vcf") || file.getName().endsWith(".VCF"));
if(useVCF)
reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new VCFCodec(), false);
else
reader = AbstractFeatureReader.getFeatureReader(file.getAbsolutePath(), new BCF2Codec(), false);
if(count%10 ==0) if(count%10 ==0)
System.out.print(count); System.out.print(count);
@ -255,13 +281,11 @@ public class CatVariants extends CommandLineProgram {
} }
System.out.println(); System.out.println();
outputStream.close();
outputWriter.close(); outputWriter.close();
return 0; return 0;
} }
public static void main(String[] args){ public static void main(String[] args){
try { try {
CatVariants instance = new CatVariants(); CatVariants instance = new CatVariants();
@ -286,5 +310,4 @@ public class CatVariants extends CommandLineProgram {
return startPositionP1 < startPositionP2 ? -1 : 1 ; return startPositionP1 < startPositionP2 ? -1 : 1 ;
} }
} }
} }