Merge pull request #2 from Blahah/master

move to Hibberdlab fork of bamtools
Merge pull request #3 from Blahah/master

update bamtools ref
first attempt at trying to do our own pileup in cpp
rewrote pileup class from scratch to just do what we want. is working now :)
Merge pull request #4 from Blahah/master

sequence segmentation implemented
added mapq to output
Merge branch 'master' into pileup
add segmentation probability
changed bin name to match transrate code
added checks for p_good; new binary
update metrics description
Merge remote-tracking branch 'upstream/master'
update mac build, add build script for osx