Merge pull request #48 from broadinstitute/dp-indels

basic indel handling in assembly, add demux pipelines
update to latest pysam
Revert "update to latest pysam"

This reverts commit 25b4ffbadb1787d22a14a3fb5c893e53426e3f7e.
update to 0.8.1, but dont include the other edits
Merge pull request #50 from broadinstitute/dp-pysam081

upgrade pysam to 0.8.1
pysam 0.8.1, etc