If the user sets the output's suffix to something different than .sam… - Githubissues

NCBI-Hackathons / NovoGraph

NovoGraph: building whole genome graphs from long-read-based de novo assemblies

MIT License

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If the user sets the output's suffix to something different than .sam… #22

Closed TorHou closed 4 years ago

TorHou commented 4 years ago

… a BAM file would be generated

evanbiederstedt commented 4 years ago

This looks quite reasonable to me.

The downstream logic of the script now requires a *.sam file. https://github.com/NCBI-Hackathons/NovoGraph/blob/master/scripts/FIND_GLOBAL_ALIGNMENTS.pl#L683-L684

I do think it's not unreasonable to remove the following as legacy code/comments, or at least put them in a different branch for library-keeping purposes. They serve little purpose in the current form for third-party users of the master branch (I think) https://github.com/NCBI-Hackathons/NovoGraph/blob/master/scripts/FIND_GLOBAL_ALIGNMENTS.pl#L666-L675

CC @AlexanderDilthey