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Sam2USeq: Prepend chr to bed regions, if it isn't there already.

TomatoFarmer: TomatoFarmer now injects a script into each cmd.txt file that determines the memory, cpus and GCThread count. Before the resources were set to the specs of the weakest nodes in our clusters. The commands also now report the the node that ran the job, which should help with future debugging.
VCFAnnotator: Added CADD scores, improved the genotype reporting in the last set of columns. VCFAnnotator should now work with FreeBayes output.

tmosbruger 2015-04-01

changed /trunk/Source/edu/utah/seq/data/Sam2USeq.java
changed /trunk/Source/edu/utah/seq/vcf/VCFAnnotator.java
changed /trunk/Source/edu/utah/seq/vcf/VCFRecord.java
changed /trunk/Source/edu/utah/seq/vcf/VCFReporter.java
changed /trunk/Source/edu/utah/seq/vcf/VCFSample.java
changed /trunk/Source/edu/utah/tomato/TomatoFarmer.java
changed /trunk/Source/edu/utah/tomato/model/TFCommand.java
changed /trunk/Source/edu/utah/tomato/model/command/TFCommandExomeVariant.java
/trunk/Source/edu/utah/seq/data/Sam2USeq.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFAnnotator.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFRecord.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFReporter.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/seq/vcf/VCFSample.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/tomato/TomatoFarmer.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/tomato/model/TFCommand.java Diff Switch to side-by-side view
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/trunk/Source/edu/utah/tomato/model/command/TFCommandExomeVariant.java Diff Switch to side-by-side view
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