segment log_r_r difference
update test.
update blessed build.
operate on the copy
keep header in intersected
InstData Import: do not pass flagstat path into helpers run flagstat methods
InstData Import: pass bam path into helpers load flagstat methods
InstData Import: change definition of is_paired_end to make sure there are actual read 1 & 2 in the bam (first 10K reads)
InstData Import: move setting instdata bam metrics to helpers
InstData Import: do not pass in bam path to update metrics
remove incorrect valid_values

These are not correct values for disk_group_name and disk_group_name
will be validated elsewhere.
add apipe_ci as valid disk group
Update the coverage stats report to allow for duplicate tumor/normal pairs.  Only uniquely report each sample/roi/processing profile combination once.  If multiple processing profiles are seen, fail.  Also allow for optional normal samples from SomaticValidation model types.
Update formatting of existing tests in BamQc.t
Add ErrorRate tests to BamQc.t
Don't run ErrorRate if aligning with bsmap
Use Set::Scalar to make an aligner blacklist
Clean up _should_run_error_rate_for_pp.

It's valid to pass undef to Set::Scalar::has() so there's no reason to
check for it.
add tagged planfile
run sciclone even if cnv_file is empty