refactoring and remove cyvcf dependencies. We will use pyvcf
add gitignore
rename binary
added plot module
bugfix. Code adapted to work with varscan and gatk call data
bugfix: count alleles count genotype type +2 properly now
update test data
move plot module to bam_crumbs. Now we depend on bam_crumbs
rename binaries. rename some ghrap title
add info to stdout about the numbers of eacg genotype
test fixed
print removed
bgzip compression and uncompression implemented
tabix indexig implemented
Illumina writer implemented
descriptive illumina writer error added
Illumina writer binary created
bugfix in high variable region filter
bugfix in the window hrev filter calculation
change typecode in the arrays used in the data_structures.
Do not collect maf is maf is None