Properly report failure to run the MergedAssembledCallsets script

If that script isn't executable, report that failure to this script's STDERR
rather than the MergedAssembledCallsets's stderr.
remove hardcoded paths to these scripts
have child query only look at allocation_path
Update aligner index debug message in Bwamem/Bwasw
child & parent allocations generate error_messages
fixing small indel bug
updated graphite submodule to 9fc8b86
use select 1 in disk allocation child query
Ignore new microarray_cnv directory when finding the cnvs.hq file.
Blithely update expected cases since a new build was run.
further fixes and improvements to clin-seq snv-indel reporting
Updated `genome` tab completion.
new somatic variation build used in clinseq

couple of things  - new somatic variation build has different
variants, changes to bam read counts by chris miller and changes to the
DV2 filter might be causing the diffs with the previous blessed build.
Update status messages so they reflect what is happening.
Merge branch 'updated' into gb_master