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CatVariants accepts reference files ending in any standard extension 

-- [resolves #49339235] Make CatVariants accept reference files ending in .fa (not only .fasta)
This commit is contained in:
Mark DePristo 2013-06-19 11:10:36 -04:00
parent 6a5502c94a
commit 15171c07a8
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();
logger.setLevel(Level.INFO);
if ( ! refFile.getName().endsWith(".fasta")) {
throw new UserException("Reference file "+refFile+"name must end with .fasta");
final ReferenceSequenceFile ref;
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();
@ -203,8 +201,6 @@ public class CatVariants extends CommandLineProgram {
if (!(outputFile.getName().endsWith(".vcf") || outputFile.getName().endsWith(".VCF"))){
throw new UserException(String.format("Output file %s should be <name>.vcf", outputFile));
}
ReferenceSequenceFile ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(refFile);
FileOutputStream outputStream = new FileOutputStream(outputFile);
EnumSet<Options> options = EnumSet.of(Options.INDEX_ON_THE_FLY);