Initial commit
initial commit of Bryce's source code
commented and cleaned up a code a bit
fixed errors in combined_test.py and added to README
Merge branch 'master', remote-tracking branch 'origin'
updates to README
Update README.md
Updated README to include more introduction etc.
better exception handling, added verbose flag to control output, corrected parsing of NAs, fix potential divide by 0
Added dependencies section to README
added example input file
Merge branch 'master' of github.com:gmcvicker/CHT
Added brief description of input file, link to dsQTL input files.
fix description of AS read counts in README
Fixes typo of the total read depth overdispersion parameter
Fixes bug of always using 0 for the geno_haps
Merge pull request #1 from glennsb/fixes

Fixes from glennsb: 
- fix typo in readme 
- fix bug where haplotypes being set to 0 incorrectly
added script which we use to generate input files for CHT
Added script to update heterozygote probabilities based on all data types
Fixed update_het_probs.py