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Better handling of fasta files with non-standard extensions.x 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1206 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
hanna 2009-07-09 18:18:48 +00:00
parent 5e26770634
commit 60a86fb34a
1 changed files with 17 additions and 1 deletions
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18
java/src/org/broadinstitute/sting/utils/fasta/IndexedFastaSequenceFile.java
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@ -22,6 +22,7 @@ import net.sf.samtools.SAMTextHeaderCodec;
import net.sf.samtools.SAMFileHeader;
import net.sf.samtools.SAMSequenceRecord;
import net.sf.samtools.util.AsciiLineReader;
import org.broadinstitute.sting.utils.StingException;
/**
* Created by IntelliJ IDEA.
@ -64,7 +65,7 @@ public class IndexedFastaSequenceFile implements ReferenceSequenceFile {
private void loadDictionary( File fastaFile ) {
// Try and locate the dictionary
String dictionaryName = fastaFile.getAbsolutePath();
dictionaryName = dictionaryName.substring(0, dictionaryName.lastIndexOf(".fasta"));
dictionaryName = dictionaryName.substring(0, getFastaFileExtensionStart(dictionaryName));
dictionaryName += ".dict";
final File dictionary = new File(dictionaryName);
if (!dictionary.exists())
@ -85,6 +86,21 @@ public class IndexedFastaSequenceFile implements ReferenceSequenceFile {
}
/**
* Gets the index of the first character in the fasta file's extension.
* @param filename The filename of the fasta. Must not be null, and must end with either '.fasta' or '.fa'.
* @return The index of the start of the extension within the filename. If neither '.fasta' nor '.fa' are
* present in the filename, a StingException will be thrown.
*/
private int getFastaFileExtensionStart( String filename ) {
if( filename.endsWith(".fasta") )
return filename.lastIndexOf(".fasta");
else if( filename.endsWith(".fa") )
return filename.lastIndexOf(".fa");
else
throw new StingException("Invalid fasta filename; fasta filename must end with '.fasta' or '.fa'.");
}
/**
* Loads the index for the fasta, if present. Throws an exception if now present.
*/