Added script to update heterozygote probabilities based on all data types
Fixed update_het_probs.py
Added script to update expected read depth based on GC content and overall reads coming from that region
Updated update_total_depth.py
added scripts for importing allele-specific counts from BAM files into HDF5 tracks
Merge branch 'master' of github.com:gmcvicker/CHT
Allows coefficients to be read from input file/ written
- No longer perform filtering of reads that is done upstream by WASP mapper
- Allow spliced reads
- Make specification of haplotypes optional
Merge branch 'master' of github.com:gmcvicker/CHT
allow data type to be specified as uint8 or uint16 on command line
allow multiple regions to be tested for single snp, multiple ways of output AS counts when test SNP is homozygous
updated usage in comments at top of file
automatically set track stats on newly created track counts
removed statement that meant script only ran on chr22 (added for testing)
bugfix total region read counts were not being computed correctly
fixes to make pulling hets from haplotype tab work, added several related command line args
make 2nd and 3rd columns in samples file optional
Adds a shebang
allows the geno_haps to be NA as well