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brianwalenz

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Commits on Feb 11, 2020

• Extend lookup to handle multiple DBs and multiple inputs, consolidate include/exclude to the same function.

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  e1d9ff4

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• Set defaults for covGap and lopsided.

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  8b1d9d1

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• Add a description of the algorithm.

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  660fb69

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• More faster and more correcter shift register searching.

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  91d6606

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• Add functions to expand pairs of bits to triples of bits.

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  committed
  7e269cf

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• Add a bunch of optimized versions for searching, realize that addition in GF(4) is xor. Lots of crud in this version though.

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  5dde89c

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Commits on Feb 10, 2020

• Skip the zeroth read in some loops.

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  1c521cf

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• Add some extra logging, some disabled.

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  1cb0a1b

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• Fix error computing how much of a potential bubble is covered by overlaps.

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  e1f89c6

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Commits on Feb 6, 2020

• Fix sneaky error checking fwrite() error codes. Issues marbl#1600, marbl#1603 and many others.

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  63bf485

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• Fix the shift register.

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  8febfac

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Commits on Jan 29, 2020

• Add debug option '-D bestOverlaps' to write an ovStore with the overlaps used for BestOverlapGraph.

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  committed
  cf01240

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• Add (secret) options for changing BestOverlapGraph parameters.

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  committed
  b4c9d8c

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• Make the ovOverlap seqStore pointer private.

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  committed
  0f63898

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• Reset the ovOverlap seqStore pointer only if it's set in the ovStore.

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  92f779d

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• Increase error rate display to 3 digits (in pictures); fix type in command line usage.

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  committed
  1fb1f1f

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• Move 'read alignment failure' log to 'algorithm debug' level output.

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  7e58304

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• Add a minimum length filter option.

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  4b39279

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Commits on Jan 23, 2020

• Add experimental filtering of short overlaps relative to read length.

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  833bbfa

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Commits on Jan 21, 2020

• A thread aware class for writing log files.

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  5e233cc

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• Make writeBuffer::flush() a public method.

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  85fffd3

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Commits on Jan 13, 2020

• Remove references to 'suspicious' reads; these are coverage-gap reads now. Output a '-' for non-mutual-best edges in asm.best.edges (to preserve column indices for each row).

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  76fee97

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Commits on Jan 9, 2020

• Add support for using pigz instead of gzip, if available.

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  9ef2ec7

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Commits on Jan 7, 2020

• Fix a race condition in lopsided reads, make sure lopsided and coverageGap aren't being inconsistent.

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  163a7f0

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• Add logging of coverageGap reads.

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  committed
  301941d

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• Cleanup ChunkGraph a bit. Fix minor bugs involving reads and read ends that don't exist (trimmed out, or no overlaps off the read end, respectively).

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  committed
  bf783a2

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• Just some simple innocent comments.

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  committed
  0ade767

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• Filter out high-error (above -eg) when computing best edge error rate.

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  f887f2c

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Commits on Jan 6, 2020

• Remove unused boost include.

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  63fcda1

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• Just a boring comment on why strings are split in two.

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  committed
  bc9c7d2

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Commits on Dec 11, 2019

• Fix calculation of overlap length for contained reads when testing if a read is fully covered by overlaps.

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  committed
  a5d2ffe

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Commits on Dec 5, 2019

• Fix for 'negative intervals' when marking repeats on reads; remove option to use bubble/spur tigs as repeat evidence.

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  committed
  14af248

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• Actually save the inverted list if the original list was empty.

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  committed
  06c4b4d

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• Don't add length zero intervals; correct for negative intervals too.

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  committed
  78b7c2e

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Commits on Dec 4, 2019

• Simplify and cleanup the intervalList; split out intervalDepth from it.

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