Initial memory hungry version of disambiguate
Memory efficient version that uses name sorted BAM files
Changed input parameters and output file names in disambiguate.py
Added counter to disambiguation process.
Added BWA option for disambiguation. Switched to using print() function.
Implemented bwa criteria for disambiguation based on tags AS, NM and XS
Fixed counting bugs for number of unique reads going to the different files.
Now checking if the intermediate name sorted BAM file already exists
summary text file name changed to match sample name
added docopt and modified __doc__ in disambiguate.py
Fixed inconsistencies in variable naming
Bug fix in input argument checking
not not bug fix
added __init__.py
MIT license included
Fixed .bam bug when including .bam in prefix
Merge branch 'master' of https://github.com/mjafin/disambiguate
Added information to README.md