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Commits on Nov 18, 2014

• Merge pull request bigdatagenomics#481 from fnothaft/run-assembly-once

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• [ADAM-480] Switch assembly to single goal.

  fnothaft

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• Merge pull request bigdatagenomics#487 from fnothaft/unhardcode-viz

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• [ADAM-486] Add port option to viz command.

  fnothaft

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Commits on Nov 17, 2014

• Merge pull request bigdatagenomics#469 from laserson/ADAM-461

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  fnothaft

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• [ADAM-461] Fix ReferenceRegion and ReferencePosition impl

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  laserson

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• Merge pull request bigdatagenomics#440 from laserson/ADAM-439

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  fnothaft

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• [ADAM-439] Fix ADAM to account for BDG-FORMATS-35

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Commits on Nov 15, 2014

• Reverting README.md back to 17d1d4d.

  fnothaft

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Commits on Nov 14, 2014

• Merge pull request bigdatagenomics#470 from erictu/master

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  fnothaft

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• Merge pull request bigdatagenomics#468 from ryan-williams/loading

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  fnothaft

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• refactor RDD loading; explicitly load alignments

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  ryan-williams

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• added ReferenceMapping for Genotype

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  erictu

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• Merge pull request bigdatagenomics#474 from massie/docs

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Commits on Nov 13, 2014

• Consolidate documentation into a single location in source.

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Commits on Nov 12, 2014

• Merge pull request bigdatagenomics#471 from neurons/fix_readme

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  massie

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• Fixed typo on MAVEN_OPTS quotation mark

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Commits on Nov 7, 2014

• Merge pull request bigdatagenomics#467 from ryan-williams/fastq

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  fnothaft

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• fastq-writing bug-fixes and cleanups

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  ryan-williams

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• Merge pull request bigdatagenomics#451 from ryan-williams/view

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  massie

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• Merge pull request bigdatagenomics#466 from allenday/master

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Commits on Nov 6, 2014

• count_kmer examle

  

  @allenday

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• link raw sam test file

  

  @allenday

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• adam-local becomes adam-submit

  

  @allenday

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• working examples on .sam included in repo

  

  @allenday

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Commits on Nov 5, 2014

• Add a test for new view command

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  ryan-williams

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• expose non-file-saving bits of adam view

  ryan-williams

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• expose non-file-saving bits of adam transform

  ryan-williams

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• add "disjunction" -g / -G options to adam view

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  ryan-williams

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• add -c, -o flags, plus opt. printing SAM to stdout

  ryan-williams

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• add adam view command

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  ryan-williams

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• helper to get SAM output as a string

  ryan-williams

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• Merge pull request bigdatagenomics#458 from massie/reads2ref

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  fnothaft

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• Remove unused val from Reads2Ref

  massie

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• Merge pull request bigdatagenomics#438 from ryan-williams/paired-fastq

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