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samtools / htsjdk

A Java API for high-throughput sequencing data (HTS) formats.
http://samtools.github.io/htsjdk/
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Tribble indexing complex files fails #1428

Closed jonn-smith closed 4 years ago

jonn-smith commented 4 years ago

In GATK, indexing using the XsvLocatableCodec is now failing.

This is because this codec works off a config file that then points to another file that contains the data. The FeatureCodec::getPathToDataFile method is designed to handle this, but it is not being called in IndexFactory::FeatureIterator.

This needs to be fixed asap or we can't index XsvLocatable features.