Implements C++ API for Bifrost - Githubissues

bacpop / unitig-caller

Methods to determine sequence element (unitig) presence/absence

Apache License 2.0

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Implements C++ API for Bifrost #7

Closed samhorsfield96 closed 3 years ago

samhorsfield96 commented 3 years ago

Updates to command-line running of unitig-caller:

Removes --build function, bifrost graphs built implicitly by Bifrost API
Implements --call, which returns unitigs within existing graph
Updates input --refs format for --simple, now takes same format as --call and --query
Updates unitigs input format for --query and --simple, do now take both fasta and txt file with one unitig per line (with header)
Removes graph pruning and inexact kmer matching functionality to simplify running

Updates to implementation:

Updates seqan3 implementation from 3.0.0 to 3.0.2 (conda version)
Implements Bifrost API, replacing system calls for Bifrost