UCSC provide a whole set of binary tools for file viewing and manipulation:

These include

• wigToBigWig
• samtools

The problem is that these are not available for Windows. However, they can be built using cygwin. The source should be downloaded from

http://hgdownload.cse.ucsc.edu/admin/exe/

It is suggested that this is only done for 64 bit machines using the cygwin 64bit toolchain as many of the tools will be unusable within a 32 bit address space.

The default build includes debug info (-g) and does not do a full optimisation (-O2). To override, the code should be built using

make CFLAGS=-O3 COPT=-O3

Some additional cygwin modules may well be required in order to build the code, particularly:

• libmysqld-devel
• libpng-devel

The mysql should pull in the zlib library which is also required. If it does not then there does not appear to be a 64bit cygwin zlib library, but loading the zlib-devel source, building it and then moving libz.a to /lib should fix the problem.