fix syntax for study lookup
Merge pull request #59 from andrewjpage/no_pending_lanes

fix syntax for study lookup
Merge branch 'VertebrateResequencing-master'
Merge branch 'master' of git+ssh://github.com/sanger-pathogens/update_pipeline

Conflicts:
	lib/IRODS/Study.pm
pull in reference
Merge pull request #61 from andrewjpage/save_reference

pull in reference
add support to import cram files
Merge pull request #62 from andrewjpage/save_reference

add support to import cram files
default to bam
Merge pull request #63 from andrewjpage/master

default to bam
change target param to end of search
Merge pull request #64 from andrewjpage/change_study_param_order

change target param to end of search
least specific to most specific speeds up irods query
Merge pull request #65 from andrewjpage/speedup_study_query

least specific to most specific speeds up irods query
travis CI
dont populate md5 if its already done
Merge pull request #66 from andrewjpage/speedup_md5

Speedup md5
make sure there are no duplicate filenames
Merge pull request #67 from andrewjpage/speedup_md5

make sure there are no duplicate filenames
filter rows