Patch to deal correctly with '=' and 'X' CIGAR flags. Updated version number.
Started adding htslib support

Added the htsLib alongside samtools. Idea will be to migrate to htsLib
for CRAM support. Also included a python skeleton for htsLib.
Removed some Cython decorators, and fixed a couple of minor bugs in the
strand bias and coverage calculations.
some changes in variantcaller.pyx
Merge branch 'master' of https://github.com/andyrimmer/Platypus
removed endBufferSize=8 when running in HLA typing mode
Merge branch 'master' of ssh://github.com/hangphan/Platypus
fix bug with haplotype generation for HLA typing
changes to chaplotype.pyx , alignmentscore cap for HLA typing