--- a
+++ b/deepvariant/dv_constants.py
@@ -0,0 +1,159 @@
+# 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.
+"""
+
+from deepvariant.protos import deepvariant_pb2
+
+# 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 = 100
+
+# Default channels if none are provided
+PILEUP_DEFAULT_CHANNELS = [
+    'read_base',
+    'base_quality',
+    'mapping_quality',
+    'strand',
+    'read_supports_variant',
+    'base_differs_from_ref',
+]
+
+# Channels that include insert size.
+PILEUP_CHANNELS_WITH_INSERT_SIZE = [
+    'read_base',
+    'base_quality',
+    'mapping_quality',
+    'strand',
+    'read_supports_variant',
+    'base_differs_from_ref',
+    'insert_size',
+]
+
+# Not a default because it's hard-coded into the code.
+PILEUP_NUM_CHANNELS = len(PILEUP_DEFAULT_CHANNELS)
+
+# 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
+NUM_DENOVO_CLASSES = 2
+
+# Default sample name if no sample name is found from the BAM header.
+DEFAULT_SAMPLE_NAME = 'default'
+
+# Define all available channels, configured using --channel_list
+CHANNELS = [
+    'read_base',
+    'base_quality',
+    'mapping_quality',
+    'strand',
+    'read_supports_variant',
+    'base_differs_from_ref',
+    'haplotype',
+    'allele_frequency',
+    'diff_channels_alternate_allele_1',
+    'diff_channels_alternate_allele_2',
+    'read_mapping_percent',
+    'avg_base_quality',
+    'identity',
+    'gap_compressed_identity',
+    'gc_content',
+    'is_homopolymer',
+    'homopolymer_weighted',
+    'blank',
+    'insert_size',
+    'base_channels_alternate_allele_1',
+    'base_channels_alternate_allele_2',
+    'mean_coverage',
+]
+
+ALT_ALIGNED_PILEUP_CHANNELS = [
+    'base_channels_alternate_allele_1',
+    'base_channels_alternate_allele_2',
+    'diff_channels_alternate_allele_1',
+    'diff_channels_alternate_allele_2',
+]
+
+# Create list of channels that can be used with --channel_list by removing
+# channels specified using --alt_aligned_pileup.
+USER_SET_CHANNELS = [
+    x for x in CHANNELS if x not in ALT_ALIGNED_PILEUP_CHANNELS
+]
+
+CHANNEL_ENUM_TO_STRING = {
+    deepvariant_pb2.CH_READ_BASE: 'read_base',
+    deepvariant_pb2.CH_BASE_QUALITY: 'base_quality',
+    deepvariant_pb2.CH_MAPPING_QUALITY: 'mapping_quality',
+    deepvariant_pb2.CH_STRAND: 'strand',
+    deepvariant_pb2.CH_READ_SUPPORTS_VARIANT: 'read_supports_variant',
+    deepvariant_pb2.CH_BASE_DIFFERS_FROM_REF: 'base_differs_from_ref',
+    deepvariant_pb2.CH_HAPLOTYPE_TAG: 'haplotype',
+    deepvariant_pb2.CH_ALLELE_FREQUENCY: 'allele_frequency',
+    deepvariant_pb2.CH_DIFF_CHANNELS_ALTERNATE_ALLELE_1: (
+        'diff_channels_alternate_allele_1'
+    ),
+    deepvariant_pb2.CH_DIFF_CHANNELS_ALTERNATE_ALLELE_2: (
+        'diff_channels_alternate_allele_2'
+    ),
+    deepvariant_pb2.CH_READ_MAPPING_PERCENT: 'read_mapping_percent',
+    deepvariant_pb2.CH_AVG_BASE_QUALITY: 'avg_base_quality',
+    deepvariant_pb2.CH_IDENTITY: 'identity',
+    deepvariant_pb2.CH_GAP_COMPRESSED_IDENTITY: 'gap_compressed_identity',
+    deepvariant_pb2.CH_GC_CONTENT: 'gc_content',
+    deepvariant_pb2.CH_IS_HOMOPOLYMER: 'is_homopolymer',
+    deepvariant_pb2.CH_HOMOPOLYMER_WEIGHTED: 'homopolymer_weighted',
+    deepvariant_pb2.CH_BLANK: 'blank',
+    deepvariant_pb2.CH_INSERT_SIZE: 'insert_size',
+    deepvariant_pb2.CH_BASE_CHANNELS_ALTERNATE_ALLELE_1: (
+        'base_channels_alternate_allele_1'
+    ),
+    deepvariant_pb2.CH_BASE_CHANNELS_ALTERNATE_ALLELE_2: (
+        'base_channels_alternate_allele_2'
+    ),
+    deepvariant_pb2.CH_MEAN_COVERAGE: 'mean_coverage',
+}
+
+# Used only when phasing is on (phase_reads=true). It allows to set the
+# region padding as a percantage over the region length. candidates are
+# calculated over an extended region. Output examples are not affected by
+# this value.
+PHASE_READS_REGION_PADDING_PCT = 20