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gumson
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Feb 3, 2026
| if (!Files.isDirectory(this.referenceFolder)) { | ||
| throw new GorResourceException("Can not create FolderReferenceSource %s as the target is not a folder or does not exists".formatted(referenceFolder), referenceFolder); | ||
| } | ||
| scanReferenceFolder(); |
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Not a fan, but have done this many times :)
gumson
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Feb 3, 2026
| referencePath, referencePath.md5(), referenceFolder)); | ||
| } | ||
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| return rsFile.getSequence(referencePath.contig()).getBases(); |
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Does this open and close the file? Is the underlying file default in a closed state?
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This at least opens it, we close all the files in the map at the end. I followd the pattern used in FastaFileReferenceSource.
gumson
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Feb 3, 2026
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Very good implementation! Approved!
gmagnu
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ENGKNOW-3046-enable-cram-binding-to-correct-reference-genome-for-exome-cloud-bfx
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