unitig-caller v1.3.0

This removes seqan3 and replaces with sdsl-lite-3, as in ggcaller, as seqan3 changed their API again. Parallelisation in simple mode is now done with openmp rather than C++ stdlib threads, so is probably a bit better.

What's Changed

• Update azure to the new repo url by @johnlees in #15
• Change seqan3 for FM-index from sdsl-lite by @johnlees in #14
• Fix for OS X compilation by @johnlees in #16

Full Changelog: v1.2.1...v1.3.0

unitig-caller v1.2.1

This is mostly a rebuild to use the new versions of bifrost (1.0.6) and seqan3 (3.1.0). The latter is a breaking change in older versions because one of the included headers has been renamed.
Bifrost tests have been slightly updated and are less strict than before.

unitig-caller v1.2.0

Update to use the bifrost C++ API, rather than calls on the command line (#7).
[Thanks to @samhorsfield96]

Also simplifies the use, you can just use --call to replicate the behaviour of unitig-counter.

Use Bifrost graphs

Additions thanks to @samhorsfield96:

• Replace squeakr and mantis with Bifrost
• Allow the Bifrost option both to count and call unitigs

Search reverse complement

v1.0.0 in --simple mode did not include rev-comp search. This is fixed here.

Use of FM-index

Overhaul simple mode to use FM-index provided by SeqAn3

Initial working release

Fixed a bug in mantis wrapper, and adds in other options.
conda recipe should be working, still need to add to bioconda (pending updated release of squeakr)

First release

Contains both modes, which have worked with a small test set
Automatically builds and installs C++ extension