Remove entire Bio::PopGen namespace and related modules, scripts, and test
commit23cb82995cc47dc7b88355730c7bdfc5a6d1c09e
authorCarnë Draug <carandraug+dev@gmail.com>
Mon, 10 Sep 2018 11:36:18 +0000 (10 12:36 +0100)
committerCarnë Draug <carandraug+dev@gmail.com>
Mon, 10 Sep 2018 11:36:18 +0000 (10 12:36 +0100)
tree3b8aa3017776d77a32da0dc42ed9b95d3e23baa5
parentb0f8c89c474692c857615796a2bbc0743957657b
Remove entire Bio::PopGen namespace and related modules, scripts, and test

These are a modular unit so they are now a separate repo named
Bio-PopGen (not yet released).  The Bio::Tree::AlleleNode has also
been moved since it is related to Bio::PopGen, dependent on it, and
not used anywhere else.

Also moved the scripts bp_composite_LD and bp_heterogeneity_test.
42 files changed:
Bio/PopGen/Genotype.pm [deleted file]
Bio/PopGen/GenotypeI.pm [deleted file]
Bio/PopGen/HtSNP.pm [deleted file]
Bio/PopGen/IO.pm [deleted file]
Bio/PopGen/IO/csv.pm [deleted file]
Bio/PopGen/IO/hapmap.pm [deleted file]
Bio/PopGen/IO/phase.pm [deleted file]
Bio/PopGen/IO/prettybase.pm [deleted file]
Bio/PopGen/Individual.pm [deleted file]
Bio/PopGen/IndividualI.pm [deleted file]
Bio/PopGen/Marker.pm [deleted file]
Bio/PopGen/MarkerI.pm [deleted file]
Bio/PopGen/PopStats.pm [deleted file]
Bio/PopGen/Population.pm [deleted file]
Bio/PopGen/PopulationI.pm [deleted file]
Bio/PopGen/Simulation/Coalescent.pm [deleted file]
Bio/PopGen/Simulation/GeneticDrift.pm [deleted file]
Bio/PopGen/Statistics.pm [deleted file]
Bio/PopGen/TagHaplotype.pm [deleted file]
Bio/PopGen/Utilities.pm [deleted file]
Bio/Tree/AlleleNode.pm [deleted file]
Changes
examples/popgen/parse_calc_stats.pl [deleted file]
scripts/popgen/bp_composite_LD.pl [deleted file]
scripts/popgen/bp_heterogeneity_test.pl [deleted file]
t/PopGen/Coalescent.t [deleted file]
t/PopGen/HtSNP.t [deleted file]
t/PopGen/MK.t [deleted file]
t/PopGen/PopGen.t [deleted file]
t/PopGen/PopGenSims.t [deleted file]
t/PopGen/TagHaplotype.t [deleted file]
t/Tree/Node.t
t/data/CG11099.fasaln [deleted file]
t/data/CG2865.fasaln [deleted file]
t/data/T7.aln [deleted file]
t/data/compLD_missingtest.prettybase [deleted file]
t/data/compLD_test.prettybase [deleted file]
t/data/example.hap [deleted file]
t/data/example.phase [deleted file]
t/data/popgen_saureus.dat [deleted file]
t/data/popgen_saureus.multidat [deleted file]
t/data/popstats.prettybase [deleted file]