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Commits on Jun 6, 2013
  1. merge development

    glennhickey committed Jun 6, 2013
Commits on Jun 5, 2013
  1. implement logic to filter small sequences via the minSeqFrac paramete…

    …r which is currently set to quarter the step size by default
    glennhickey committed Jun 5, 2013
  2. params

    glennhickey committed Jun 5, 2013
Commits on Jun 4, 2013
  1. remove ifstream error checking because it wont work with udc. note th…

    …ese errors will get checked in the halapi anyway
    glennhickey committed Jun 4, 2013
  2. change lod manager to open alignments only when needed. change block …

    …api to always query dna strings from the coarsest level of detail
    glennhickey committed Jun 4, 2013
  3. add --probeFrac option to sample ranges of step intervals looking for…

    … most aligned positions
    glennhickey committed Jun 4, 2013
  4. undo last change where median was used for delta. go back to using ma…

    …x but base it on total distance to both neighbours and compare to step instead of using max neighbour and comparing to half step
    glennhickey committed Jun 4, 2013
Commits on Jun 3, 2013
  1. adjust default param values for lod creation. reactive trans in hal2a…

    …ssembly up and change scale and maxblock in lodInterpolate
    glennhickey committed Jun 3, 2013
  2. remove compiler warning

    glennhickey committed Jun 3, 2013