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Replace Bio::DB::Fasta with faidx_xs

Marek Szuba requested to merge github/fork/willmclaren/feature/faidx into master

Created by: willmclaren


  • can index bgzipped FASTA files (though note Ensembl distributes gzipped, must be converted to bgzipped before use). Human toplevel file is ~1.1g bgzipped, 40g uncompressed.
  • indexes much more robust, won't tolerate corrupted/partial index like Bio::DB::Fasta
  • around 10x faster retrieving sequence


The .travis.yml install of htslib and faidx_xs is non-ideal as it avoids using "make install" by compiling the module into the home directory. Much better if you have sudo access to do "make install" properly for each.

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