Satmut-utils

Added back run_design_conversion.py to prototype directory

Added __init__.py to prototype directory. Now in package.

Fixed URL links in setup.cfg and in satmut_utils_manual.md to point to ijhoskins repo

Fixed variant calling bug that caused di-nt MNPs to be called as two SNPs when the di-nt MNP was downstream of a single SNP or another di-nt MNP.

Fixed variant calling bug that caused di-nt MNPs to be called as two SNPs when the di-nt MNP was downstream of a single SNP or another di-nt MNP

Fixed bug where default --nthreads argument causes variant calling to fail during consensus deduplication.

Added minimum versions for dependencies. Download satmut_utils from pip during creation of conda environment.

Fixed links to point to ijhoskins repo in installation script

Fixed links to manual in README.md to point to ijhoskins