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PureCLIP 1.1.0
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@skrakau skrakau released this 07 Aug 20:57
· 46 commits to master since this release
v1.1.0
6391506

  • Fixed bug in HMM application part concerning the elimination of intervals containing emission probabilities of 0.0. Whole interval is discarded now.

  • Fixed floating point error in normalisation of left-truncated gamma distribution.

  • Minor fix regarding content and filename of model parameter output. User parameter '-p' is applied now, or '.params' is appended to base of crosslink site output filename.

  • Changed floating point precision for various intermediate computations.

  • Added error handling regarding emission probabilities getting close precision limits.

  • Changed initialisation of gamma distributions. Nelder-Mead simplex algorithm is applied directly to multidimensional problem and restarted for different start values. For the gamma GLM initialisation first parameters are estimated for the compound gamma distribution. Based on these start values are chosen for the 'non-enriched' and 'enriched' simplex procedure and state posterior probabilities are assigned based on the expected value.

  • Changed handling of parameter constraints in combination with the simplex algorithm. Instead of fixing gamma shape parameter values when the algorithm is running out of constraints, the likelihood landscape outside of the constraints and seen by the GSL simplex algorithm is modified and penalties depending on the distance are applied. Gamma mean values are estimated in log-space.

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