switch to csi index - Githubissues

EI-CoreBioinformatics / reat

Robust Eukaryotic Annotation Toolkit

https://reat.readthedocs.io/en/latest/

MIT License

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Closed swarbred closed 2 years ago

swarbred commented 2 years ago

Currently in reat prediction call-FirstStrandIndexBAM we create the default bai index this will error with mappings to large genomes such as wheat.

We can hopefully switch to generating the csi index in all cases (samtools index -c)

we use the index in call-FirstStrandHints/bam2hints