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Restore ReferenceSequenceFileFactory deleted in previous commit. #1743

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Merged
merged 2 commits into from
Apr 22, 2025
Merged

Restore ReferenceSequenceFileFactory deleted in previous commit. #1743

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f3442bb
Restore ReferenceSequenceFileFactory method previously deleted.
cmnbroad Apr 14, 2025
e276fbd
Remove redundant code.
cmnbroad Apr 22, 2025
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41 changes: 25 additions & 16 deletions src/main/java/htsjdk/samtools/reference/ReferenceSequenceFileFactory.java
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Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,29 @@ public static ReferenceSequenceFile getReferenceSequenceFile(final Path path, fi
return getReferenceSequenceFile(path, HtsPath::new, truncateNamesAtWhitespace, true);
}

/**
* Attempts to determine the type of the reference file and return an instance
* of ReferenceSequenceFile that is appropriate to read it.
*
* @param path the reference sequence file path
* @param truncateNamesAtWhitespace if true, only include the first word of the sequence name
* @param preferIndexed if true attempt to return an indexed reader that supports non-linear traversal, else return the non-indexed reader
*/
public static ReferenceSequenceFile getReferenceSequenceFile(final Path path, final boolean truncateNamesAtWhitespace, final boolean preferIndexed) {
// this should thrown an exception if the fasta file is not supported
getFastaExtension(path);
// Using faidx requires truncateNamesAtWhitespace
if (truncateNamesAtWhitespace && preferIndexed && canCreateIndexedFastaReader(path)) {
try {
return IOUtil.isBlockCompressed(path, true) ? new BlockCompressedIndexedFastaSequenceFile(path) : new IndexedFastaSequenceFile(path);
} catch (final IOException e) {
throw new SAMException("Error opening FASTA: " + path, e);
}
} else {
return new FastaSequenceFile(path, truncateNamesAtWhitespace);
}
}

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Maybe this can just delegate to the new method.

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@cmnbroad cmnbroad Apr 22, 2025 •
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Fixed. Well, I restored the old method and changed the new one to delegate to the old one.

/**
* Attempts to determine the type of the reference file and return an instance
* of ReferenceSequenceFile that is appropriate to read it. If the file represents
Expand All @@ -148,22 +171,8 @@ public static <T extends IOPath> ReferenceSequenceFile getReferenceSequenceFile(
if (refIOPath.hasExtension(BundleJSON.BUNDLE_EXTENSION)) {
final Bundle referenceBundle = BundleJSON.toBundle(IOUtils.getStringFromPath(refIOPath), ioPathConstructor);
return getReferenceSequenceFileFromBundle(referenceBundle, truncateNamesAtWhitespace, preferIndexed);
}
else {
// this should throw an exception if the fasta file is not supported
getFastaExtension(path);
// Using faidx requires truncateNamesAtWhitespace
if (truncateNamesAtWhitespace && preferIndexed && canCreateIndexedFastaReader(path)) {
try {
return IOUtil.isBlockCompressed(path, true) ?
new BlockCompressedIndexedFastaSequenceFile(path) :
new IndexedFastaSequenceFile(path);
} catch (final IOException e) {
throw new SAMException("Error opening FASTA: " + path, e);
}
} else {
return new FastaSequenceFile(path, truncateNamesAtWhitespace);
}
} else {
return getReferenceSequenceFile(path, truncateNamesAtWhitespace, preferIndexed);
}
}

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