Added initial set of tools for sequencing
Now has a genome context
now has an HIV specific genome context
now actually commiting the new code.
added some utility functions for testing the alignments. Taken from the AsanaController project.
added new conda recipes for alignment tools
Now has the basic reference alignment tools
added more conda-recipies
change to tox.ini to make sure py.test doesn't check the conda-recipies directories for tests
now can slice sam records
now install bcftools through an annoying hack
changing the samtools and bcftools to the newest release. Its eaiser then dealing with the crapy version inconsitencies
because I'm bad at bash!
Added tools to deal with the Variant Caller format. Needed a lot of work to get the right conda-packages built properly!
improved some docs
had to include binaries of samtools and bcftools due to versioning issues. The build_env.py auto-handles the install of these.
fixed the version issue with samtools and bcftools
debugging travis issues
maybe changing the path?
align_to_genome now can dump the sorted-bam file to a path in case the file is too large to fit in limitted memory