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Merge pull request #293 from broadinstitute/md_catvariants 

CatVariants accepts reference files ending in any standard extension
This commit is contained in:
amilev 2013-06-19 08:36:58 -07:00
parent 6a5502c94a 15171c07a8
commit 28a8d74290
1 changed files with 5 additions and 9 deletions
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14
public/java/src/org/broadinstitute/sting/tools/CatVariants.java
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@ -144,15 +144,13 @@ public class CatVariants extends CommandLineProgram {
BasicConfigurator.configure(); BasicConfigurator.configure();
logger.setLevel(Level.INFO); logger.setLevel(Level.INFO);
if ( ! refFile.getName().endsWith(".fasta")) { final ReferenceSequenceFile ref;
throw new UserException("Reference file "+refFile+"name must end with .fasta"); try {
ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(refFile);
} catch ( Exception e ) {
throw new UserException("Couldn't load provided reference sequence file " + refFile, e);
} }
if ( ! refFile.exists() ) {
throw new UserException(String.format("Reference file %s does not exist", refFile.getAbsolutePath()));
}
// Comparator<Pair<Integer,FeatureReader<VariantContext>>> comparator = new PositionComparator();
Comparator<Pair<Integer,File>> positionComparator = new PositionComparator(); Comparator<Pair<Integer,File>> positionComparator = new PositionComparator();
@ -203,8 +201,6 @@ public class CatVariants extends CommandLineProgram {
if (!(outputFile.getName().endsWith(".vcf") || outputFile.getName().endsWith(".VCF"))){ if (!(outputFile.getName().endsWith(".vcf") || outputFile.getName().endsWith(".VCF"))){
throw new UserException(String.format("Output file %s should be <name>.vcf", outputFile)); throw new UserException(String.format("Output file %s should be <name>.vcf", outputFile));
} }
ReferenceSequenceFile ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(refFile);
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);