Split out contig names from Reference .fai file on white space (to support the GATK resource bundle's file human_g1k_v37.fasta.fai.gz, which does not use tab delimiters)
First preliminary big refactoring of UG annotation engine. Goals: a) Remove gigantic hack that cached per-read haplotype likelihoods in a static array so that annotations would go back and retrieve them, b) unify interface for annotations between HaplotypeCaller and UnifiedGenotyper, c) as a consequence, removed and cleaned duplicated code. As a bonus, annotations have now more relevant info to help them compute values.
Major idea is that per-read haplotype likelihoods are now stored in a single unified object of class PerReadAlleleLikelihoodMap. Class implementation in theory hides internal storage details from outside work (still may need work cleaning up interface), and this object(or rather, a Map from Sample->perReadAlleleLikelihoodMap) is produced by UGCalcLikelihoods. The genotype calculation is also able to potentially use this info if needed. All InfoFieldAnnotations now get an extra argument with this map. Currently, this map is only produced for indels in UG, or for all variants within HaplotypeCaller. If this map is absent (SNPs in UG), the old Pileup interface is used, but it's avoided whenever possible. FORMAT annotations are not yet changed but will be focus of second step. Major benefit will be that annotations will be able to very easily discard non-informative reads for certain events. HaplotypeCaller also uses this new class, and no longer hard-codes the mapping of allele ->list(reads) but instead uses the same objects and interfaces as the rest of the modules. Code still needs further testing/cleaning/reviewing/debugging
Fix merge conflicts
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Second step of interface cleanup for variant annotator: several bug fixes, don't hash pileup elements to Maps because the hashCode() for a pileup element is not implemented and strange things can happen. Still several things to do, not done yet
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Next iteration of new VA interface: extend changes to per-genotype annotations as well. Will allow to have AD correctly implemented at last (that change not done yet)
Another round of FindBugs fixes. Inefficient use of keySet iterator instead of entrySet iterator.
Another round of FindBugs fixes. Should be static inner class.
Another round of FindBugs fixes. Class implements its own compareTo() but uses base Object.equals() which can lead to unpredictable behavior.
New implementation of AD - ignore now non-informative reads based on per-read likelihoods
Fixing merge conflicts
Re-enabling parallelism in the BaseRecalibrator now that the release is out.
Changed the default memory limit from none to 2GB upon suggestions from delangel, carneiro, and depristo.
Merged bug fix from Stable into Unstable
 number of stashed changes are lurking in here. In order of importance:
 - Fix for M_Trieb's error report on the forum, and addition of integration tests to cover the walker.
 - Addition of StructuralIndel as a class of variation within the VariantContext. These are for variants with a full alt allele that's >150bp in length.
 - Adaptation of the MVLikelihoodRatio to work for a set of trios (takes the max over the trios of the MVLR)
 - InsertSizeDistribution changed to use the new gatk report output (it was previously broken)
 - RetrogeneDiscovery changed to be compatible with the new gatk report
 - A maxIndelSize argument added to SelectVariants
 - ByTranscriptEvaluator rewritten for cleanliness
 - VariantRecalibrator modified to not exclude structural indels from recalibration if the mode is INDEL
 - Documentation added to DepthOfCoverageIntegrationTest (no, don't yell at chartl ;_; )

Also sorry for the long commit history behind this that is the result of fixing merge conflicts. Because this *also* fixes a conflict (from git stash apply), for some reason I can't rebase all of them away. I'm pretty sure some of the commit notes say "this note isn't important because I'm going to rebase it anyway".
Another round of FindBugs fixes. Comparator doesn't implement Serializable.
Another round of FindBugs fixes. Object internally stores a reference to an externally mutable array. Very dangerous.
Another round of FindBugs fixes. Object returns its internal reference to an externally mutable array. Very dangerous.