Merge pull request #113 from hammerlab/pair-info

Add pair info and insert size to read; Add insert size filter
updates to filters
Merge pull request #114 from hammerlab/filter-extra

Adding overlapping deletion filter and fixes to others
add pair alignment information to read
Merge pull request #115 from hammerlab/paired-read-info

Add pair alignment information to read
init somatic logodds caller
more updates to somatic log odds