Update included samtools and boost

[serge2016]

Hello!
Is it possible not build included samtools and boost but use already existing in the system? Is it possible to pass some kind of flags pointing to directories with them?

[seqfu]

For the next release we'll be on samtools 1.x, previous versions were using 0.x, so this should be possible. For Boost, the included code is a small subset and there may be version dependencies (it might even be modified), not sure.

[serge2016]

Let it be only samtools 1.1x! But why not to use that installed instance of samtoots, that already exists? Many users already have samtools installed, that's why it sounds reasonable to use it...

[serge2016]

If bam-readcount works with exact version of boost - ok, but again, using external one sounds reasonable. If there are modifications in boost's code - then it is more complicated... But what are these modifications?