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NCBI-Hackathons / NovoGraph

NovoGraph: building whole genome graphs from long-read-based de novo assemblies
MIT License
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Remove Bio::DB::HTS #28

Closed evanbiederstedt closed 4 years ago

evanbiederstedt commented 4 years ago

Remove use of Bio::DB::HTS, the Perl interface to HTSlib

https://metacpan.org/release/Bio-DB-HTS

evanbiederstedt commented 4 years ago

As I mentioned, there is one last bit to change, whereby we iterate through the QNAMEs.

The method/subroutine features() is explained here: https://metacpan.org/pod/Bio::DB::HTS#@alignments-=-$segment-%3Efeatures(%args)

There is a way to do this without an HTSlib wrapper, but I currently think my piping scheme will be slower than simply using Bio::DB::HTS….I didn't try it out, to be honest.

@AlexanderDilthey may have some thoughts

I'm happy to keep the library for this task.

evanbiederstedt commented 4 years ago

Development on countExpectedGlobalAlignments.pl will take a bit longer, so I put this in another branch.

Feel free to review @TorHou and merge