v2.4.0 - More representative BigWig output

Previous versions of the bamToBw.pl script included all reads in the input BAM/CRAM in the counts. Historically all of the common tools for generating these files have done this. With the introduction of several new flags for BWA-mem the data becomes skewed (particularly by supplimentary reads).

This release filters reads where the flags overlap with 3844

• 4 - read unmapped
• 256 - Not primary alignment
• 512 - read fails platform/vendor quality checks
• 1024 - read is PCR or optical duplicate
• 2048 - supplementary alignment

See: explain-flags

We plan to expose the parameter in the future so please add support to the issue #121 if you want to be able to control this value.