Apart from fixing the Makefile and the README.md, the main change is the ability for binUnsorted to process BED files that don't use 'chr' in the chromosome name. This is done by duplicating the keys for the map, such that both 'chr1' and '1' are valid.
Despite this, the rest of the code (namely analyze) still assumes that the BED file needs to include 'chr' in the chromosome name. I haven't changed this as I haven't tested all the options.
Apart from fixing the Makefile and the README.md, the main change is the ability for binUnsorted to process BED files that don't use 'chr' in the chromosome name. This is done by duplicating the keys for the map, such that both 'chr1' and '1' are valid.
Despite this, the rest of the code (namely analyze) still assumes that the BED file needs to include 'chr' in the chromosome name. I haven't changed this as I haven't tested all the options.