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Resolve conflicts in test files
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@kishwarshafin
kishwarshafin committed Mar 18, 2024
1 parent f575751 commit bf9ed7e
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Showing 30 changed files with 38 additions and 36 deletions.
2 changes: 1 addition & 1 deletion deepvariant/dv_vcf_constants.py
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from third_party.nucleus.util import vcf_constants

# Current release version of DeepVariant.
DEEP_VARIANT_VERSION = '1.6.0'
DEEP_VARIANT_VERSION = '1.6.1'

# FILTER field IDs.
DEEP_VARIANT_PASS = 'PASS'
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3 changes: 2 additions & 1 deletion ...ariant/testdata/customized_classes.golden.training_examples.tfrecord.gz.example_info.json
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{"version": "1.6.0", "shape": [100, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
{"version": "1.6.1", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}

2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.allele_frequency_examples.tfrecord.gz.example_info.json
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{"version": "1.6.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 8]}
{"version": "1.6.1", "shape": [100, 221, 8], "channels": [1, 2, 3, 4, 5, 6, 19, 8]}
2 changes: 1 addition & 1 deletion ...t/testdata/golden.alt_aligned_pileup_diff_channels_examples.tfrecord.gz.example_info.json
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{"version": "1.6.0", "shape": [100, 221, 8], "channels": [1, 2, 3, 4, 5, 6, 9, 10]}
{"version": "1.6.1", "shape": [100, 221, 8], "channels": [1, 2, 3, 4, 5, 6, 9, 10]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.alt_aligned_pileup_rows_examples.tfrecord.gz.example_info.json
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{"version": "1.6.0", "shape": [300, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
{"version": "1.6.1", "shape": [300, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.calling_examples.tfrecord.gz-00000-of-00003.example_info.json
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{"version": "1.6.0", "shape": [100, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
{"version": "1.6.1", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.calling_examples.tfrecord.gz-00001-of-00003.example_info.json
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{"version": "1.6.0", "shape": [100, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
{"version": "1.6.1", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.calling_examples.tfrecord.gz-00002-of-00003.example_info.json
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{"version": "1.6.0", "shape": [100, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
{"version": "1.6.1", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.calling_examples.tfrecord.gz.example_info.json
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{"version": "1.6.0", "shape": [100, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
{"version": "1.6.1", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.postprocess_gvcf_output.g.vcf
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Expand Up @@ -12,7 +12,7 @@
##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.6.0
##DeepVariant_version=1.6.1
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 10000000 . T <*> 0 . END=10000116 GT:GQ:MIN_DP:PL 0/0:50:45:0,135,1349
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2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.postprocess_gvcf_output.med_dp.g.vcf
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##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.6.0
##DeepVariant_version=1.6.1
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 10000000 . T <*> 0 . END=10000116 GT:GQ:MIN_DP:MED_DP:PL 0/0:50:45:58:0,135,1349
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2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.postprocess_single_site_output.pass_only.vcf
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##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.6.0
##DeepVariant_version=1.6.1
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 10000117 . C T 36.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:34:55:25,30:0.545455:36,0,37
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2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.postprocess_single_site_output.vcf
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##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.6.0
##DeepVariant_version=1.6.1
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 10000117 . C T 36.9 PASS . GT:GQ:DP:AD:VAF:PL 0/1:34:55:25,30:0.545455:36,0,37
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2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.sv_calling_examples.tfrecord.gz.example_info.json
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{"version": "1.6.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 7]}
{"version": "1.6.1", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 7]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.training_examples.tfrecord.gz-00000-of-00003.example_info.json
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{"version": "1.6.0", "shape": [100, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
{"version": "1.6.1", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.training_examples.tfrecord.gz-00001-of-00003.example_info.json
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{"version": "1.6.0", "shape": [100, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
{"version": "1.6.1", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.training_examples.tfrecord.gz-00002-of-00003.example_info.json
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{"version": "1.6.0", "shape": [100, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
{"version": "1.6.1", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.training_examples.tfrecord.gz.example_info.json
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{"version": "1.6.0", "shape": [100, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
{"version": "1.6.1", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.training_examples.vcf
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Expand Up @@ -12,7 +12,7 @@
##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.6.0
##DeepVariant_version=1.6.1
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 10001019 . T G 0 . . GT:DP:AD:VAF 0/1:44:31,13:0.295455
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2 changes: 1 addition & 1 deletion ...nt/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz.example_info.json
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@@ -1 +1 @@
{"version": "1.6.0", "shape": [100, 221, 6], "channels": [1, 2, 3, 4, 5, 6]}
{"version": "1.6.1", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
1 change: 1 addition & 0 deletions ...ant/testdata/golden.vcf_candidate_importer_calling_examples.tfrecord.gz.example_info.json
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@@ -0,0 +1 @@
{"version": "1.6.1", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
2 changes: 1 addition & 1 deletion deepvariant/testdata/golden.vcf_candidate_importer_postprocess_single_site_output.vcf
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Expand Up @@ -12,7 +12,7 @@
##FORMAT=<ID=VAF,Number=A,Type=Float,Description="Variant allele fractions.">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Phred-scaled genotype likelihoods rounded to the closest integer">
##FORMAT=<ID=MED_DP,Number=1,Type=Integer,Description="Median DP observed within the GVCF block rounded to the nearest integer.">
##DeepVariant_version=1.6.0
##DeepVariant_version=1.6.1
##contig=<ID=chr20,length=63025520>
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
chr20 59777010 . C CCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCA 1 NoCall . GT:GQ:DP:AD:VAF:PL ./.:0:0:0,0:0:0,0
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4 changes: 2 additions & 2 deletions docs/cybdv_notebook.ipynb
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Expand Up @@ -74,10 +74,10 @@
"source": [
"<table class=\"tfo-notebook-buttons\" align=\"left\">\n",
" <td>\n",
" <a target=\"_blank\" href=\"https://colab.research.google.com/github/google/deepvariant/blob/r1.6/docs/cybdv_notebook.ipynb\"><img src=\"https://www.tensorflow.org/images/colab_logo_32px.png\" />Run in Google Colab</a>\n",
" <a target=\"_blank\" href=\"https://colab.research.google.com/github/google/deepvariant/blob/r1.6.1/docs/cybdv_notebook.ipynb\"><img src=\"https://www.tensorflow.org/images/colab_logo_32px.png\" />Run in Google Colab</a>\n",
" </td>\n",
" <td>\n",
" <a target=\"_blank\" href=\"https://github.com/google/deepvariant/blob/r1.6/docs/cybdv_notebook.ipynb\"><img src=\"https://www.tensorflow.org/images/GitHub-Mark-32px.png\" />View source on GitHub</a>\n",
" <a target=\"_blank\" href=\"https://github.com/google/deepvariant/blob/r1.6.1/docs/cybdv_notebook.ipynb\"><img src=\"https://www.tensorflow.org/images/GitHub-Mark-32px.png\" />View source on GitHub</a>\n",
" </td>\n",
"</table>"
]
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4 changes: 2 additions & 2 deletions docs/visualizing_examples.ipynb
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Expand Up @@ -35,10 +35,10 @@
"source": [
"<table class=\"tfo-notebook-buttons\" align=\"left\">\n",
" <td>\n",
" <a target=\"_blank\" href=\"https://colab.research.google.com/github/google/deepvariant/blob/r1.6/docs/visualizing_examples.ipynb\"><img src=\"https://www.tensorflow.org/images/colab_logo_32px.png\" />Run in Google Colab</a>\n",
" <a target=\"_blank\" href=\"https://colab.research.google.com/github/google/deepvariant/blob/r1.6.1/docs/visualizing_examples.ipynb\"><img src=\"https://www.tensorflow.org/images/colab_logo_32px.png\" />Run in Google Colab</a>\n",
" </td>\n",
" <td>\n",
" <a target=\"_blank\" href=\"https://github.com/google/deepvariant/blob/r1.6/docs/visualizing_examples.ipynb\"><img src=\"https://www.tensorflow.org/images/GitHub-Mark-32px.png\" />View source on GitHub</a>\n",
" <a target=\"_blank\" href=\"https://github.com/google/deepvariant/blob/r1.6.1/docs/visualizing_examples.ipynb\"><img src=\"https://www.tensorflow.org/images/GitHub-Mark-32px.png\" />View source on GitHub</a>\n",
" </td>\n",
"</table>"
]
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2 changes: 1 addition & 1 deletion scripts/inference_deepsomatic.sh
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Expand Up @@ -74,7 +74,7 @@ SAVE_INTERMEDIATE_RESULTS=false
BAM_NORMAL=""
BAM_TUMOR=""
DOCKER_SOURCE="google/deepsomatic"
BIN_VERSION="1.6.0"
BIN_VERSION="1.6.1"
CALL_VARIANTS_ARGS=""
CAPTURE_BED=""
CUSTOMIZED_MODEL=""
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2 changes: 1 addition & 1 deletion scripts/inference_deeptrio.sh
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Expand Up @@ -79,7 +79,7 @@ BAM_CHILD=""
BAM_PARENT1=""
BAM_PARENT2=""
DOCKER_SOURCE="google/deepvariant"
BIN_VERSION="1.6.0"
BIN_VERSION="1.6.1"
CALL_VARIANTS_ARGS=""
CAPTURE_BED=""
CUSTOMIZED_MODEL_PARENT=""
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2 changes: 1 addition & 1 deletion scripts/inference_deepvariant.sh
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Expand Up @@ -73,7 +73,7 @@ SAVE_INTERMEDIATE_RESULTS=false
# Strings; sorted alphabetically.
BAM=""
DOCKER_SOURCE="google/deepvariant"
BIN_VERSION="1.6.0"
BIN_VERSION="1.6.1"
CALL_VARIANTS_ARGS=""
CAPTURE_BED=""
CUSTOMIZED_MODEL=""
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4 changes: 2 additions & 2 deletions scripts/run_deepsomatic.py
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Expand Up @@ -245,7 +245,7 @@

# Current release version of DeepVariant.
# Should be the same in dv_vcf_constants.py.
DEEP_VARIANT_VERSION = '1.6.0'
DEEP_VARIANT_VERSION = '1.6.1'


def _is_quoted(value):
Expand Down Expand Up @@ -540,7 +540,7 @@ def check_flags():
raise RuntimeError(
'The model files {}* do not exist. Potentially '
'relevant issue: '
'https://github.com/google/deepvariant/blob/r1.6/docs/'
'https://github.com/google/deepvariant/blob/r1.6.1/docs/'
'FAQ.md#why-cant-it-find-one-of-the-input-files-eg-'
'could-not-open'.format(_CUSTOMIZED_MODEL.value)
)
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6 changes: 3 additions & 3 deletions scripts/run_deeptrio.py
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Expand Up @@ -288,7 +288,7 @@

# Current release version of DeepTrio.
# Should be the same in dv_vcf_constants.py.
DEEP_TRIO_VERSION = '1.6.0'
DEEP_TRIO_VERSION = '1.6.1'
GLNEXUS_VERSION = 'v1.2.7'

DEEP_TRIO_WGS_PILEUP_HEIGHT_CHILD = 60
Expand Down Expand Up @@ -740,7 +740,7 @@ def check_flags():
raise RuntimeError(
'The model files {}* do not exist. Potentially '
'relevant issue: '
'https://github.com/google/deepvariant/blob/r1.6/docs/'
'https://github.com/google/deepvariant/blob/r1.6.1/docs/'
'FAQ.md#why-cant-it-find-one-of-the-input-files-eg-'
'could-not-open'.format(_CUSTOMIZED_MODEL_PARENT.value)
)
Expand All @@ -759,7 +759,7 @@ def check_flags():
raise RuntimeError(
'The model files {}* do not exist. Potentially '
'relevant issue: '
'https://github.com/google/deepvariant/blob/r1.6/docs/'
'https://github.com/google/deepvariant/blob/r1.6.1/docs/'
'FAQ.md#why-cant-it-find-one-of-the-input-files-eg-'
'could-not-open'.format(_CUSTOMIZED_MODEL_CHILD.value)
)
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6 changes: 3 additions & 3 deletions scripts/run_deepvariant.py
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Expand Up @@ -34,7 +34,7 @@
using the binaries in the Docker image.
For more details, see:
https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-quick-start.md
https://github.com/google/deepvariant/blob/r1.6.1/docs/deepvariant-quick-start.md
"""

import os
Expand Down Expand Up @@ -262,7 +262,7 @@

# Current release version of DeepVariant.
# Should be the same in dv_vcf_constants.py.
DEEP_VARIANT_VERSION = '1.6.0'
DEEP_VARIANT_VERSION = '1.6.1'


def _is_quoted(value):
Expand Down Expand Up @@ -544,7 +544,7 @@ def check_flags():
raise RuntimeError(
'The model files {}* do not exist. Potentially '
'relevant issue: '
'https://github.com/google/deepvariant/blob/r1.6/docs/'
'https://github.com/google/deepvariant/blob/r1.6.1/docs/'
'FAQ.md#why-cant-it-find-one-of-the-input-files-eg-'
'could-not-open'.format(_CUSTOMIZED_MODEL.value)
)
Expand Down

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