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New, improved, rewritten assembler#127

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fnothaft wants to merge 43 commits intobigdatagenomics:masterbigdatagenomics/avocado:masterfrom fnothaft:threaded-assemblerfnothaft/avocado:threaded-assemblerCopy head branch name to clipboard

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Commits

Commits on Apr 20, 2015

• Rewriting assembler.

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  b76b6a2

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• Assembly graph builder works for simple examples.

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  206e76d

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• Added assembly graph to observation hook.

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  cbb1810

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• Casted to tail recusive

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  b69d73d

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• Made assembler emit sample specific graphs.

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  74cbbb7

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• Removed hook for spur removal.

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  769384e

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• Recast observation enumeration to log contexts. First step in supporting graph spurs, multiallelic sites, and multiple references.

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  793596b

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• Added support for spur traversal.

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• Have multipath working.

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• Have inserts working in DeBrujin graph.

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  29262bc

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• Have deletions working.

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  5e2138c

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• Got MNP bubbles working.

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  e83c012

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• Added support for complex alleles.

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  7ff5b00

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• Got end to end assembler working.

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  57ff822

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• [avocado-97] upgraded local assembler.

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• Added documentation on assembly method.

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  2c249ba

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• Upgrading to latest ADAM.

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  e49e08c

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• Clean up region join.

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  1fdbd78

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• Added timers to local reassembler.

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  6f0ffc0

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• Add active region threshold.

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  49c362a

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• More fixes.

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  dbecf05

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• Adding config file.

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  5390b1e

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• Added code for chopping and flanking reference fragments.

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  0b743fd

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• Integrated flank creator to local assembler.

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  dc540a3

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• Small modifications to properties.

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  a3c51b8

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• Fixing deletion bookkeeping issue.

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  61248e2

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• Changing an assert to warning logging.

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  548f14d

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• Small updates to clean up complex allele parsing code.

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  f450ac8

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• Adding further instrumentation to debug.

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  459f514

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• Rewriting observation code to use preallocated array.

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  4bf21d9

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• Adding code to allow extending the observation array.

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  633401f

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• Tuning overflow threshold.

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  b6bf393

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• Miscellaneous cleanup and performance debug.

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  71ce687

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• Fixing build issues.

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  6aa29c7

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• Add loop detection logic.

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  23b9558

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• Fixing CIGAR_CODEC issue.

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  48c2b44

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• Fix to upstream change in ReferenceRegion.

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  75a81ed

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• Fix dependency.

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  2cb4008

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• Added loop detection code for reference k-mers.

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  a7e8a26

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• Make rank sum annotation optional so that it isn't applied if we do not have alt/ref observations.

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Commits on Apr 22, 2015

• Adding more debug printing.

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Commits on Apr 23, 2015

• Add serialization package.

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• Only project selected fields on load.

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