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  • Aaron's avatar
    Multiple changes. · 184656c1
    Aaron authored
    	1.  Added support for VCF 4.0.  BED.end is based on the size of the REF allele in the VCF entry.
    	2.  Fixed a bug in BamReader.cpp that bombed when seq and qual are == "*"
    	3.  Changed the Makefiles to inherit flags from the master Makefile in the root directory.
    	4.  Fixed a bug in bedToBam to created incorrect CIGAR strings for the first block.