Frank Austin Nothaft comments

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                                            Frank Austin Nothaft

Update indexer to use ananas's colored de Bruijn graph

On top of this, we won't use equivalence classes for EM, but will instead check for transcript compatibility.

any docs

We'll be adding them up as we get the pipeline up and running.

Benchmark against Precision FDA or other "truth-sets"

Yes, we have these benchmarks and a pipeline; will ping later.

Per position allele count reporting utility ( like bam-readcount)

+1! This looks like a great start. I'll make more of a pass over this later this week. Thanks for the first cut @jpdna!

Per position allele count reporting utility ( like bam-readcount)

Jenkins, add to whitelist.

Work on getting Mutect algorithm up and running

Jenkins, add to whitelist and test this please.

Work on getting Mutect algorithm up and running

Thanks for putting this together @jstjohn! I'm going to work on a harness for actually running data through this. Essentially, I think I'm going to move `org.bdgenomics.avocado.algorithms.mutect.Mutect` into the `org.bdgenomics.avocado.genotyping`...

Work on getting Mutect algorithm up and running

Jenkins, retest this please.

Work on getting Mutect algorithm up and running

Jenkins, retest this please. Looks like we have a Jenkins instance that is running Java 6. I've just modified our job setup to _not_ use that machine.