reimport lanes in update_if_changed mode for TotalReadsMismatch errors as well
fixed delete_lane() so that it actually works for UpdatePipeline::Exceptions::PathToLaneChanged exceptions
do not TotalReadsMismatch->throw if vrtrack says 0 total_reads, and set vrtrack raw_reads if currently 0
fixed logic of test to set sample individual if missing
unwithdraw lanes if they reappear in iRODS
empty vrtrack_lanes hash in -wdr mode so unwithdrawing will work
large speedup by storing sample table in class variable; _populate_supplier_name() becomes _populate_supplier_and_public_name() which is now called in populate() since it is no longer time consuming
trivial comment change, now that we get public name for sample as well
if public_name is passed in it is now set as the alias of the individual
also get individual.name and individual.alias, to allow for detecting changes in these
added detection for changes in individual name and alias, with the name test based on if use_supplier_name is in effect
added public_name as a property
fixed unecessary unwithdrawing
pull from upstream master
fixed undefined variable issues
Merge branch 'master' of github.com:sanger-pathogens/update_pipeline into vertres
lower default num reads
Merge pull request #51 from andrewjpage/lower_minimum_reads

lower default num reads
Merge branches 'vertres' and 'master'
Merge branch 'master' of git+ssh://github.com/sanger-pathogens/update_pipeline

Conflicts:
	modules/UpdatePipeline/UpdateLaneMetaData.pm