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New, improved, rewritten assembler #127

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wants to merge 43 commits into from
Closed

New, improved, rewritten assembler #127

wants to merge 43 commits into from

Commits on Apr 20, 2015

  1. Rewriting assembler.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  2. Assembly graph builder works for simple examples.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  3. Added assembly graph to observation hook.

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    fnothaft committed Apr 20, 2015
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  4. Casted to tail recusive

    @fnothaft
    fnothaft committed Apr 20, 2015
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  5. Made assembler emit sample specific graphs.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  6. Removed hook for spur removal.

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    fnothaft committed Apr 20, 2015
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  7. Recast observation enumeration to log contexts. First step in support… 

    …ing graph spurs, multiallelic sites, and multiple references.
    @fnothaft
    fnothaft committed Apr 20, 2015
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  8. Added support for spur traversal.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  9. Have multipath working.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  10. Have inserts working in DeBrujin graph.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  11. Have deletions working.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  12. Got MNP bubbles working.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  13. Added support for complex alleles.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  14. Got end to end assembler working.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  15. [avocado-97] upgraded local assembler.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  16. Added documentation on assembly method.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  17. Upgrading to latest ADAM.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  18. Clean up region join.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  19. Added timers to local reassembler.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  20. Add active region threshold.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  21. More fixes.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  22. Adding config file.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  23. Added code for chopping and flanking reference fragments.

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    fnothaft committed Apr 20, 2015
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  24. Integrated flank creator to local assembler.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  25. Small modifications to properties.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  26. Fixing deletion bookkeeping issue.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  27. Changing an assert to warning logging.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  28. Small updates to clean up complex allele parsing code.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  29. Adding further instrumentation to debug.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  30. Rewriting observation code to use preallocated array.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  31. Adding code to allow extending the observation array.

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    fnothaft committed Apr 20, 2015
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  32. Tuning overflow threshold.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  33. Miscellaneous cleanup and performance debug.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  34. Fixing build issues.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  35. Add loop detection logic.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  36. Fixing CIGAR_CODEC issue.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  37. Fix to upstream change in ReferenceRegion.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  38. Fix dependency.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  39. Added loop detection code for reference k-mers.

    @fnothaft
    fnothaft committed Apr 20, 2015
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  40. Make rank sum annotation optional so that it isn't applied if we do n… 

    …ot have alt/ref observations.
    @fnothaft
    fnothaft committed Apr 20, 2015
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Commits on Apr 22, 2015

  1. Adding more debug printing.

    @fnothaft
    fnothaft committed Apr 22, 2015
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Commits on Apr 23, 2015

  1. Add serialization package.

    @fnothaft
    fnothaft committed Apr 23, 2015
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  2. Only project selected fields on load.

    @fnothaft
    fnothaft committed Apr 23, 2015
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