Adding Convey HC-1 HMM acceleration
Disable CnyPairHMM
Added command-line flag to disble FPGA
Completed integration with FPGA driver
Don't crash if cds file is not provided

CDS file should be optional.
better docs for Qualify Missing Intervals

now that it's available to the public, better give'em good docs!
Merge branch 'master' into st_fpga_hmm

Conflicts:
	protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
	protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
Remove debug print statement
VariantRecalibrator bugfix for bad log10sumlog10 values

-- The VR, when the model is bad, may evaluate log10sumlog10 where some of the values in the vector are NaN. This case is now trapped in VR and handled as previously -- indicating that the model has failed and evaluation continues.
Experimental LikelihoodRankSum annotation

-- Added experimental LikelihoodRankSum, which required slightly more detailed access to the information managed by the base class, so added an overloaded getElementForRead also provides access to the MostLikelyAllele class
-- Added base class default implementation of getElementForPileupElement() which returns null, indicating that the pileup version isn't supported.
-- Added @Override to many of the RankSum classes for safety's sake

-- Updates to GeneralCallingPipeline: annotate sites with dbSNP IDs,
-- R script to assess the value of annotations for VQSR
Another fix for the Indel Realigner that arises because of secondary alignments.

This time we don't accidentally drop reads (phew), but this bug does cause us not to
update the alignment start of the mate.  Fixed and added unit test to cover it.
Merge pull request #299 from broadinstitute/eb_mate_fixer_confused_by_nonprimary_alignment

Another fix for the Indel Realigner that arises because of secondary alignments.
Merge pull request #300 from broadinstitute/mc_move_qualify_intervals_to_protected

Few bug fixes to this tool now that it is in protected
quick fixes to the scala script

   * Increase the memory limit for HTSLIB - Bam shuffling just eats up a ton of memory.
   * Concurrent HTSLIB processes need unique temp files the bam shuffling step was messing up with the temporary files and failing without returning zero. Fixed it by giving a unique name to each process.
Merge pull request #302 from broadinstitute/mc_processing_pipeline2

quick updates to the techdev processing pipeline scala script
Merged bug fix from Stable into Unstable
Fixing the 'header is negative' problem in Reduce Reads... again.

Previous fixes and tests only covered trailing soft-clips.  Now that up front
hard-clipping is working properly though, we were failing on those in the tool.

Added a patch for this as well as a separate test independent of the soft-clips
to make sure that it's working properly.
Merge pull request #304 from broadinstitute/eb_rr_header_negative_fix_again

Fixing the 'header is negative' problem in Reduce Reads... again.
Various updates to have the KB use the expanded exome intervals (from D MacArthur) in addition to chr20.

1. MergeIntervalLists should take the global interval padding into account when merging.
2. Update the name of the imported callsets in the setup script because of renaming for expanded intervals.
3. If there are too many intervals to process, MongoDB falls apart.  Refactored the site selection code so
   that in such cases we pull out all records from the DB and the GATK itself does the interval filtering.
4. Add isComplex to callset summary for the consensus summarizer.
5. Remove the check for out of order records in the SiteIterator since records now do come out of order
  (since contigs are sorted lexicographically in MongoDB).

Results:
Iteration over the gencode intervals (90 MB) in AssessNA12878 now takes 90 seconds.  I can't tell you how
much time it took before because it kept crashing Mongo (but it was a long, long time).
Merge pull request #303 from broadinstitute/eb_update_kb_to_use_exome_intervals

Various updates to have the KB use the expanded exome intervals (from D ...
Move DownsampleReadsQC walker to private