Merge pull request #147 from tcarver/master

misc
Merge pull request #148 from tcarver/master

misc
use INFILE command line option
Merge pull request #149 from tcarver/master

misc
Merge pull request #150 from tcarver/master

rename
Merge pull request #151 from tcarver/master

mics
Merge pull request #152 from tcarver/master

misc
Merge pull request #153 from tcarver/master

misc
Merge pull request #154 from tcarver/master

update version
Merge pull request #155 from tcarver/master

bamview update
Merge pull request #156 from tcarver/master

misc
Merge pull request #157 from tcarver/master

misc
Merge pull request #158 from tcarver/master

misc
Merge pull request #159 from tcarver/master

misc
Merge pull request #160 from tcarver/master

misc
Merge pull request #161 from tcarver/master

misc
Merge pull request #162 from tcarver/master

misc
Merge pull request #163 from tcarver/master

misc
Merge pull request #164 from tcarver/master

update
Merge pull request #165 from tcarver/master

misc