merge from develop resolving conflicts
add method to bam filetype to check magic easily
add step and test for GATK reduce reads
temporary debugging disable of server start and stop
fixed mistake in previous conflict resolution
now correctly handles searching with DateTime objects
when getting setups via the fork_call, use dbic freeze and thaw so we do not lose the schema
base quality score recalibration for GATK v2
test for bqsr and reduce reads pipelines
step, pipeline and test for gatk haplotype caller
Merge branch 'develop' of /software/vertres/git/origin/vr-pipe into feature/bqsr
Merge branch 'feature/bqsr' into develop
rename steps and pipelines from previous commit for consistency
rename again
fix name method
corrected instructions on how to fix a bad 0.103 upgrade
further corrected instructions on how to fix a bad 0.103 upgrade
added ability to disable_inflation in get_column_values
use POSIX since we use ceil() now
corrected instructions on how to fix a bad 0.103 upgrade