Removed mapping error rate from estimate of denoised copy ratios outp…

…ut by gCNV and updated sklearn.
broadinstitute · May 19, 2021 · cb2ab69 · cb2ab69
1 parent 4cccab3
commit cb2ab69
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Showing 3 changed files with 3 additions and 4 deletions.
diff --git a/scripts/gatkcondaenv.yml.template b/scripts/gatkcondaenv.yml.template
@@ -38,7 +38,7 @@ dependencies:
                                     #   if you wish to update, note that versions of conda-forge::keras after 2.2.5
                                     #   undesirably set the environment variable KERAS_BACKEND = theano by default
 - defaults::intel-openmp=2019.4
-- conda-forge::scikit-learn=0.22.2
+- conda-forge::scikit-learn=0.23.1
 - conda-forge::matplotlib=3.2.1
 - conda-forge::pandas=1.0.3
 

diff --git a/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_denoising_calling.py b/src/main/python/org/broadinstitute/hellbender/gcnvkernel/models/model_denoising_calling.py
@@ -786,8 +786,7 @@ def __init__(self,
         # the expected number of erroneously mapped reads
         mean_mapping_error_correction_s = eps_mapping * read_depth_s * shared_workspace.average_ploidy_s
 
-        denoised_copy_ratio_st = ((shared_workspace.n_st - mean_mapping_error_correction_s.dimshuffle(0, 'x'))
-                                  / ((1.0 - eps_mapping) * read_depth_s.dimshuffle(0, 'x') * bias_st))
+        denoised_copy_ratio_st = shared_workspace.n_st / (read_depth_s.dimshuffle(0, 'x') * bias_st)
 
         Deterministic(name='denoised_copy_ratio_st', var=denoised_copy_ratio_st)
 

diff --git a/...est/java/org/broadinstitute/hellbender/utils/python/PythonEnvironmentIntegrationTest.java b/...est/java/org/broadinstitute/hellbender/utils/python/PythonEnvironmentIntegrationTest.java
@@ -25,7 +25,7 @@ public Object[][] getDataPackagePresent() {
                 { "pymc3",          "3.1" },
                 { "keras",          "2.2.4" },
                 { "h5py",           "2.10.0" },
-                { "sklearn",        "0.22.2.post1" },
+                { "sklearn",        "0.23.1" },
                 { "matplotlib",     "3.2.1" },
                 { "pandas",         "1.0.3" },
                 { "argparse",       null },