MauricioCarneiro/PairHMM

Issues

• Possible misalignment in PairHMM evaluation

  #35 opened 7 years ago by DavideSampietro
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• PairhmmImpl receives Diagonal class implementation via template

  #29 opened 10 years ago by MauricioCarneiro
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• Add generic aligned allocator with modified padding allocation (and memset to 0)

  #30 opened 10 years ago by MauricioCarneiro
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• pass padded_haplotypes to recalculate

  #26 opened 11 years ago by MauricioCarneiro
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• move diagonal related methods to the diagonal class

  #27 opened 11 years ago by MauricioCarneiro
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• remove hpp implementations (standardization)

  #31 opened 11 years ago by MauricioCarneiro
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• add m_ to all class members

  #28 opened 11 years ago by MauricioCarneiro
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• Check the minimum and maximum values in the matrix

  #8 opened 11 years ago by MauricioCarneiro
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• Separate cell update into three stages (increasing i, steady-state, decreasing i)

  #12 opened 11 years ago by MauricioCarneiro
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• implement updateCell in unidimensional mode

  #13 opened 11 years ago by MauricioCarneiro
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• Redesign the test routine to be more realistic

  #16 opened 11 years ago by MauricioCarneiro
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• Make a branch for barcoding and include Michael Ross

  #17 opened 11 years ago by MauricioCarneiro
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• Redesign the API to retro-fit the HC calls

  #15 opened 12 years ago by MauricioCarneiro
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• Fix hapStartIndex -- right now it won't work, or won't use it properly.

  #14 opened 12 years ago by MauricioCarneiro
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• Pull out d and e calculations into a pre-init routine

  #11 opened 12 years ago by MauricioCarneiro
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• Implement a diagonal with prob values (get rid of log values and log sums) using exponent (2^) for each diagonal

  #9 opened 12 years ago by MauricioCarneiro
  2

• hapStartIndex is not working with new implementation

  #10 opened 12 years ago by MauricioCarneiro
  2

• Prepare a 'real life' workload for HMM testing based on a Haplotype Caller run

  #1 opened 12 years ago by MauricioCarneiro
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• Can we add sentinels to the ends of the matrix ? (readBases.length + 1)

  #4 opened 12 years ago by MauricioCarneiro
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• Pre-add the sentinel values for row and column = 0

  #3 opened 12 years ago by MauricioCarneiro
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• Pre-convert Phred-scaled values to ErrorProb and only reconvert once

  #2 opened 12 years ago by MauricioCarneiro
  1

• updateCell should get d,e arrays instead of GOPs and GCPs (only depends on i)

  #6 opened 12 years ago by MauricioCarneiro
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• Use Math.min on qualIndexGOP calculation instead of double if

  #5 opened 12 years ago by MauricioCarneiro
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• approximateLog10SumLog10 doesn't need an "or"

  #7 opened 12 years ago by MauricioCarneiro
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