Fast and simple haplotype counting.
Only sbt is required; it handles the rest. Once it is installed:
git clone https://github.com/gabrielkg/croissant.git
cd croissant
sbt "runMain Croissant --help"
Will download dependencies, compile and run. You should eventually see something like:
[info] welcome to sbt 1.5.5 (Oracle Corporation Java 1.8.0_202)
[info] loading settings for project croissant-build from plugins.sbt ...
[info] loading project definition from /group/home/gk0a/temp/croissant/project
[info] loading settings for project croissant from build.sbt ...
[info] set current project to croissant (in build file:/group/home/gk0a/temp/croissant/)
[info] running Croissant --help
Croissant 0.3 (c) 2015-2021 Gabriel Keeble-Gagnere, Agriculture Victoria
-a, --alignment <arg> Sorted BAM alignment file
-c, --cov-only Only report coverage (no haplotype information)
-m, --mp Aligned data is mate pair
-v, --verbose
-w, --window <arg> Number of mismatches around target to consider in
haplotype calculation
-h, --help Show help message
--version Show version of this program