initial
added new script
No more git stuff in script and now logging to screen and file
consensus generation
Tests are good
tests tests
tests directory module thing
flagstats
Merge branch 'master' of /home/EIDRUdata/Tyghe/Dev/undocumented
Reads are now paired by their mate if possible
compile reads tested
About to move to a class decorator for mock objects
yay patch decorators are fun
bwa_mem seems to be working
Added relative and absolute paths to tests just for fun. InvalidRead now includes the read file path that caused it
Creating a new module for read specific stuffs and putting compile_reads in there
bam.py has samtobam and is testes
sortbam working
Merge branch 'master' of /home/EIDRUdata/Tyghe/Dev/undocumented
indexbam working