bhammer: support multiple libraries
bhammer: Fix exception message
spades: correctly use single end reads
Merge branch 'master' of github.com:kbase/assembly into cb
bwa: merges SAM on multiple libraries
ArastDataInputeError
bowtie2: merge SAMs on mixed reads
dynamically set bwa threads
Merge branch 'master' of github.com:kbase/assembly into cb
remove pipe requirement
Merge branch 'master' of github.com:kbase/assembly into cb
add appdirs
Merge branch 'master' of github.com:kbase/assembly into cb
ArastDataOututError
reapr update, use smalt
add test for mixed-lib input
remove legacy function _get_data_old() which is no longer called