add module for Samtools pipeline
add stubs for tasks and sub commands
make functions private and add inputs and outputs to tasks
add command names to subcommands
add subtask support for commands
redirect subcommands final output to a file
add parameter and input file support
refactor function to generate subcommands
generate subcommands with flags
add task generation
add pipeline generation
Set defaults for jobs missing fields
fix path and pipeline generation
add multiple snp pipeline support
remove duplicate comma
move to_filename into the Utils module
move tasks into Task

	modified:   modules/Pipelines/lib/CoGe/Pipelines/SNP/Samtools.pm
	renamed:    modules/Pipelines/lib/CoGe/Pipelines/SNP/Samtools.pm -> modules/Pipelines/lib/CoGe/Pipelines/SNP/Tasks.pm
add annotation support to load_experiment
add platypus pipeline
add fasta index job