Added clarifying message and removed unneeded comments
Added shortcut method to Command/WithSoftwareResult
gmt dindel run-with-vcf no longer takes model-id as input
Add shellcmd_arrayref to Genome::Sys

This allows you to pass an arrayref of strings and they will
be escaped properly (for example, filenames with spaces in them)

Of course we could just use 'system' but would lose all the
other things that Genome::Sys->shellcmd gives us.
Clean up RealignCandidates

Rename output_file to output_prefix to better explain what it does
Give it an output so we can use it in workflows
Added skeleton of xml for RealignWithVcf
Fleshed out unittest for RunWithVcf
GetCigarIndels inherits from Dindel::Base
Fix up RunWithVcf.t
Add base class for Dindel tools
RealignCandidates inherits from Dindel::Base
GetCigarIndels has outputs declared explicitly
make output_dindel_file an output
add a reasonable test
make output_dindel_file an output
add a reasonable test
Added python_script sub to Base
AnalyzeWindowFile inherits from Dindel::Base
MakeDindelWindows inherits from Dindel::Base
Merge branch 'AP-11' of ssh://git/srv/git/genome into AP-11