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rPHG 0.2.3

  • Fixed issue with variable evaluation in the plotDot() function

rPHG 0.2.2

  • Fixed issue with DEMO method endpoint returning incorrect dimensional data for specific Maize PHGv1 methods

rPHG 0.2.1

  • Added new function, plotDot()
    • Creates dot plots from .anchorspro files
  • Added new function, gvcfMetrics()
    • Creates summary metrics for a directory of gVCF files

rPHG 0.2.0

  • Unified workflow for both local and server instances
  • Added new class, PHGServerCon
    • New object for connecting to remote public PHG servers using BrAPI endpoints
  • Added new class, PHGLocalCon
    • New object for connecting to local SQLite or PostgreSQL database instances
  • Added new class, HaplotypeGraph
    • Wrapper for PHG API Java graph object
  • Prior objects now use method dispatch for singular set of methods to return relevant PHG data:
    • PHGMethod()
    • showPHGMethods()
    • readSamples()
    • readRefRanges()
    • readHaplotypeIds()
    • readPHGDataSet()
  • Updated summary methods:
    • numHaploPerRefRange()
    • calcMutualInfo()
    • plotGraph()
    • plotMutualInfo()

rPHG 0.1.18

  • Modified availablePHGMethods():
    • Now returns only method IDs for graphs with more than 100 samples in the data
    • This prevents publicly available testing methods to be displayed for new PHG users.

rPHG 0.1.17

  • Added new "DEMO" method parameter for PHGMethod() constructor:
    • specified as PHGMethod("DEMO")
    • Will download a small section (25 samples x 1000 reference ranges) of the Goodman/Buckler path data
    • Useful for testing and demonstrations

rPHG 0.1.16

  • Added new function, plotGraph()
    • Returns a visNetwork object for a given section of PHG data filtered by reference range
  • Updated installation information on README

rPHG 0.1.15

  • Added new function, taxaByNode()
    • Returns a tibble object of taxa IDs that are found in a group of haplotype IDs for a given set of reference range IDs
  • Update to latest jar files including PHG build

rPHG 0.1.14

  • Update logging function (startLogger())
  • Add new tests to expand code coverage
  • Deprecate BrAPI calls that use external khttp client in PHG jar

rPHG 0.1.13

  • Update to latest jar files including PHG build

rPHG 0.1.12

  • Added BrAPI endpoint methods for obtaining PHG data from BrAPI webservices:
    • BrapiCon
    • BrapiConPHG
    • readRefRanges()
    • readSamples()
    • readTable()
    • readPHGDatasetFromBrapi()
    • filterRefRanges()
    • filterSamples()
    • serverInfo()
    • availablePHGMethods()
  • Added Kotlin methods for improved data parsing speeds.
  • Added new parameters in graphBuilder()
    • buildType - do you want the graph built from paths or haplotypes?

rPHG 0.1.11

  • Added NEWS file for tracking version updates.
  • Added error checks for catching C stack usage errors for configuration file checks in functions that require configuration file path parameters.
  • Fixed edge cases in plotNumHaplo() and plotMutualInfo().