sex chrom phasing fix

fixed various bugs in autophasing for male sex chrom variants. Added new notes in readme and output to remind user of the build

fixed missing arg bug

a function call (multithread_find_many()) in informative_site_finder was missing an arg.

Stable release

With this release I've added options to modify all the previously hard-coded options for quality thresholds and so forth, although still recommend using defaults. CI should remain thus for the foreseeable future.

fixed vcf output formatting + cram support

I was annotating phasing incorrectly, so I switched to the standard method (pipes in GT field). Also added CRAM support

enhanced tests, linting

added considerable testing and performed code review and linting with isort, pyflakes, black, and flake8. Should be ready for real use now

stopped trying to support python2

python 2 is for chumps anyway. Might try again later, though

fixed backward compat issue

added missing future import of print to support python 2

improved prefix fix

previous prefix fix made readbacked fazing stop working, so this version fixes it

prefix bugfix

fixed a bug in the prefix assignment

first release

Not ready for widespead use, but useable if you really know what you're doing.