Added if statement to test for exome or WGS data. Works with WGS but not exome yet
Added exome only option to MakeCircosPlot. Will use WGS if available. If not, will use exome data. Will use WGS if both are available.
corrects regex in MakeCircosPlot.pm to work with the snv and indel files from exome, WGS, or exome and WGS
Corrects column used for sort command on top 100 gene names used for the outside circle of Circos plots
Based on suggested conflicts with PR #68
Merge branch 'trio_with_homopolymer' of https://github.com/jasonwalker80/genome into jasonwalker80-trio_with_homopolymer
Merge branch 'jasonwalker80-trio_with_homopolymer'
Merge branch 'master' of https://github.com/genome/genome
Merge branch 'master' of https://github.com/genome/genome
Merge branch 'master' of https://github.com/genome/genome
Add the GenotypeConcordance command in Picard 1.122.  Also a basic RefAlign command to generate genotype concordance from VCF files.
Whitespace.
Sanitize the chromosome name as needed for making a path
Quote the chromsome name for the shell
Print version we couldn't find instead of literal string.
Simplify shellcmd call--it always returns 1 or dies.
Remove redundant debug message.

shellcmd() already prints the cmd (as a status message) right before running it.
Check in advance for possible directory collisions.
check that "parsed" lookup_hash is valid before using
Tighten validation regex for lookup hashes.
clin-seq: when multiple data types (e.g. WGS and Exome) are available for a single sample, require that only one of these meet the minimum coverage filter