adding Ber.pm
adding Ber test and layout for new pipeline
add some more docs and sudo code
Updating Ber.pm
Update Ber.pm again
Updating Ber.pm - added setup
Quick changes to Ber
More quick changes to Ber
Added Ber.t
Updated `genome` tab completion.
Remove outdated comments.

Even if they are still relevant, shellcmd() isn't in this file.
extract duplicated bed entry parsing code into sub
skip genome browser annotation lines

The BED format as described on the UCSC has examples that contain Genome
Browser annotation lines starting with 'browser' so it seems like we
should just skip them (or maybe print them).
show line number and content when track name is unknown
refactoring of FeatureList while working on RT/98143

* pinch:
  show line number and content when track name is unknown
  skip genome browser annotation lines
  extract duplicated bed entry parsing code into sub
extract method _htseq_stranded_param
Genome::Model::Tools::Htseq::Count v2

Fixes bug reported in RT/98157 and defined new result as v2.  The only
change is in the _htseq_stranded_param so methods version by
Genome::Command::WithSavedResults are just aliased to v1.
bump default version of Htseq::Count to v2

Since v1 produces bad results the default should be bumped to v2.
Htseq::Count v2

* bump default version of Htseq::Count to v2
* Genome::Model::Tools::Htseq::Count v2
* extract method _htseq_stranded_param
remove the create functionality from get_or_create_lane_qc_models.

This behavior was deprecated by AP Config, which is now responsible for creating lane_qc models. See AUE-190 for details