Create pipeline and step to add manual qc data to bam file metadata.
fix missing ] in new writeback pipeline
Check MD5 sum matches what IRODS thinks it is BEFORE fetching file
Make error message about md5 failure more informative.
Check MD5 sum matches what IRODS thinks it is BEFORE fetching file
Make error message about md5 failure more informative.
Allow tribbles in -knownSites
Tweak requirements for bam_calculate_bq
Fix ichksum check
Draft of bamcheck_indels
Tweak bam_strip_tags
Remove experimental record counting code in favour of upstream version
HGI's autoqc tweak steps to detect quality drop off and indel spikes
Attempt to deal with mark dups out of memory segfaults
Ability to add metadata to determine which individual relates to a sample
HGI current and legacy pipelines
Various older mp15 changes for pipeline pre 2013july18
More robust handling of auto_qc config and refactoring of common
test code into test_minmax
Added use MooseX::Singleton to automatically instantiate class as a singleton
Added a sanity check as to whether there are any results before outputting them.
Merge branch 'release/0.167' into develop