merging the master branch into the banded so the banded is up to date #451
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Typo in pi at i(n-1), changed to i(n-i)
pi formula typo at i(n-1) -> changed to i(n-i)
Default behavior is changed to building and using the htslib submodule. Old default behavior was assuming systemwide installation. If HTSSRC is defined, angsd will use htslib at HTSSRC. If HTSSRC not defined, angsd will fetch, build and use the submodule.
Add GitHub Actions Workflow named "build-tests". Build tests migrated from Travis to GitHub.
Add htslib as submodule; Add GitHub Actions workflow for build test
Remove .travis.yml and replace the travis badge with GitHub actions workflow badge (shields.io)
[chore]: Remove travis, replace travis badge
Users can now choose to use the systemwide htslib installation by using `make HTSSRC=systemwide`. Default behavior is: Using `make` angsd will fetch the htslib submodule, make and use it. Users can also use `make HTSSRC=/path/to/htslib` to use the htslib of their choice, or use the systemwide htslib installation by using `make HTSSRC=systemwide`.
[feat](htslib): Add systemwide htslib option
…it was not general. Function was only used in one context and there should therefore not be any change in functionality and results
…ally, and this might show up as strange sfs when using fixed major/minor ancestral/derived ref/alt (3gl/3pls) as input.
…for the sfstest. I have commented out the specific md5sum. It is not just a difference in the compression, the uncompressed file also yield different md5sums. When looking at the actual values, the range of difference is [1] -1.421085e-14 2.842171e-14 so very small.
Changed a number of strcpy strncpy
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Preparing for merging the banded saf estimation into master branch by first merging the master branch into the banded version.