added support for build37 by ignoring GL contigs
add $! to error message
CHANGELOG Add jar_path function to locate jar files

Similar to sw_path functionality.
gatk v2.4 is available
RealignIndels is compatible with gatk2.4
Refactor how legacy versions are determined
gatk germline-snv verbose option is legacy
gatk u-g uses correct glm for non-legacy versions
Merge branch 'allpaths' into gb_master
Fix the bad GL header line in polymutt0.13
Merge branch 'master' into gb_master
Allow reference version numbers without letters
Create .detailed vcf files and trim variant detctor columns from the standard vcf

Create snvs and indels.detailed.vcf files that contain the content of the old snvs and indels.vcf files.  The new snvs and indels.vcf files have the per detector columns removed for convenience.

Ensure that the TCGA submission vcf files have the per detector columns.