--- a +++ b/deeptrio/dt_constants.py @@ -0,0 +1,60 @@ +# Copyright 2017 Google LLC. +# +# Redistribution and use in source and binary forms, with or without +# modification, are permitted provided that the following conditions +# are met: +# +# 1. Redistributions of source code must retain the above copyright notice, +# this list of conditions and the following disclaimer. +# +# 2. Redistributions in binary form must reproduce the above copyright +# notice, this list of conditions and the following disclaimer in the +# documentation and/or other materials provided with the distribution. +# +# 3. Neither the name of the copyright holder nor the names of its +# contributors may be used to endorse or promote products derived from this +# software without specific prior written permission. +# +# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE +# ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE +# LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR +# CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF +# SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS +# INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN +# CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) +# ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE +# POSSIBILITY OF SUCH DAMAGE. +"""Common constants shared across DeepVariant's codebase. + +This file is for very general constants in the code that end up needing to be +accessed in a variety of places, often in live code as well as throughout the +code in tests. +""" + +# Default width [in basepairs] for our DeepVariant data tensor. +PILEUP_DEFAULT_WIDTH = 221 + +# Default height [in rows] for our DeepVariant data tensor. +PILEUP_DEFAULT_HEIGHT = 300 + +# Default height [in rows] for our DeepVariant parent data tensor. +PILEUP_DEFAULT_HEIGHT_PARENT = 100 + +# Default height [in rows] for our DeepVariant child data tensor. +PILEUP_DEFAULT_HEIGHT_CHILD = 100 + +# Not a default because it's hard-coded into the code. +PILEUP_NUM_CHANNELS = 6 + +# The dimensions of a pileup image tensor as height x width x rank. +PILEUP_DEFAULT_DIMS = [ + PILEUP_DEFAULT_HEIGHT, + PILEUP_DEFAULT_WIDTH, + PILEUP_NUM_CHANNELS, +] + +# Number of classes represented in the data set. The three classes are +# homozygous reference (0), heterozygous (1) and homozygous alternative (2). +NUM_CLASSES = 3