Resolve conflicts in test files

google · Mar 18, 2024 · bf9ed7e · bf9ed7e
1 parent f575751
commit bf9ed7e
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Showing 30 changed files with 38 additions and 36 deletions.
diff --git a/deepvariant/dv_vcf_constants.py b/deepvariant/dv_vcf_constants.py
@@ -32,7 +32,7 @@
 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'

diff --git a/...ariant/testdata/customized_classes.golden.training_examples.tfrecord.gz.example_info.json b/...ariant/testdata/customized_classes.golden.training_examples.tfrecord.gz.example_info.json
@@ -1 +1,2 @@
-{"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]}
+
diff --git a/deepvariant/testdata/golden.allele_frequency_examples.tfrecord.gz.example_info.json b/deepvariant/testdata/golden.allele_frequency_examples.tfrecord.gz.example_info.json
@@ -1 +1 @@
-{"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]}
diff --git a/...t/testdata/golden.alt_aligned_pileup_diff_channels_examples.tfrecord.gz.example_info.json b/...t/testdata/golden.alt_aligned_pileup_diff_channels_examples.tfrecord.gz.example_info.json
@@ -1 +1 @@
-{"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]}
diff --git a/deepvariant/testdata/golden.alt_aligned_pileup_rows_examples.tfrecord.gz.example_info.json b/deepvariant/testdata/golden.alt_aligned_pileup_rows_examples.tfrecord.gz.example_info.json
@@ -1 +1 @@
-{"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]}
diff --git a/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00000-of-00003.example_info.json b/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00000-of-00003.example_info.json
@@ -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]}
diff --git a/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00001-of-00003.example_info.json b/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00001-of-00003.example_info.json
@@ -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]}
diff --git a/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00002-of-00003.example_info.json b/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00002-of-00003.example_info.json
@@ -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]}
diff --git a/deepvariant/testdata/golden.calling_examples.tfrecord.gz.example_info.json b/deepvariant/testdata/golden.calling_examples.tfrecord.gz.example_info.json
@@ -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]}
diff --git a/deepvariant/testdata/golden.postprocess_gvcf_output.g.vcf b/deepvariant/testdata/golden.postprocess_gvcf_output.g.vcf
@@ -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

diff --git a/deepvariant/testdata/golden.postprocess_gvcf_output.med_dp.g.vcf b/deepvariant/testdata/golden.postprocess_gvcf_output.med_dp.g.vcf
@@ -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:MED_DP:PL	0/0:50:45:58:0,135,1349

diff --git a/deepvariant/testdata/golden.postprocess_single_site_output.pass_only.vcf b/deepvariant/testdata/golden.postprocess_single_site_output.pass_only.vcf
@@ -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	10000117	.	C	T	36.9	PASS	.	GT:GQ:DP:AD:VAF:PL	0/1:34:55:25,30:0.545455:36,0,37

diff --git a/deepvariant/testdata/golden.postprocess_single_site_output.vcf b/deepvariant/testdata/golden.postprocess_single_site_output.vcf
@@ -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	10000117	.	C	T	36.9	PASS	.	GT:GQ:DP:AD:VAF:PL	0/1:34:55:25,30:0.545455:36,0,37

diff --git a/deepvariant/testdata/golden.sv_calling_examples.tfrecord.gz.example_info.json b/deepvariant/testdata/golden.sv_calling_examples.tfrecord.gz.example_info.json
@@ -1 +1 @@
-{"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]}
diff --git a/deepvariant/testdata/golden.training_examples.tfrecord.gz-00000-of-00003.example_info.json b/deepvariant/testdata/golden.training_examples.tfrecord.gz-00000-of-00003.example_info.json
@@ -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]}
diff --git a/deepvariant/testdata/golden.training_examples.tfrecord.gz-00001-of-00003.example_info.json b/deepvariant/testdata/golden.training_examples.tfrecord.gz-00001-of-00003.example_info.json
@@ -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]}
diff --git a/deepvariant/testdata/golden.training_examples.tfrecord.gz-00002-of-00003.example_info.json b/deepvariant/testdata/golden.training_examples.tfrecord.gz-00002-of-00003.example_info.json
@@ -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]}
diff --git a/deepvariant/testdata/golden.training_examples.tfrecord.gz.example_info.json b/deepvariant/testdata/golden.training_examples.tfrecord.gz.example_info.json
@@ -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]}
diff --git a/deepvariant/testdata/golden.training_examples.vcf b/deepvariant/testdata/golden.training_examples.vcf
@@ -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

diff --git a/...nt/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz.example_info.json b/...nt/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz.example_info.json
@@ -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]}
diff --git a/...ant/testdata/golden.vcf_candidate_importer_calling_examples.tfrecord.gz.example_info.json b/...ant/testdata/golden.vcf_candidate_importer_calling_examples.tfrecord.gz.example_info.json
@@ -0,0 +1 @@
+{"version": "1.6.1", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]}
diff --git a/deepvariant/testdata/golden.vcf_candidate_importer_postprocess_single_site_output.vcf b/deepvariant/testdata/golden.vcf_candidate_importer_postprocess_single_site_output.vcf
@@ -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

diff --git a/docs/cybdv_notebook.ipynb b/docs/cybdv_notebook.ipynb
@@ -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>"
       ]

diff --git a/docs/visualizing_examples.ipynb b/docs/visualizing_examples.ipynb
@@ -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>"
       ]

diff --git a/scripts/inference_deepsomatic.sh b/scripts/inference_deepsomatic.sh
@@ -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=""

diff --git a/scripts/inference_deeptrio.sh b/scripts/inference_deeptrio.sh
@@ -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=""

diff --git a/scripts/inference_deepvariant.sh b/scripts/inference_deepvariant.sh
@@ -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=""

diff --git a/scripts/run_deepsomatic.py b/scripts/run_deepsomatic.py
@@ -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):
@@ -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)
       )

diff --git a/scripts/run_deeptrio.py b/scripts/run_deeptrio.py
@@ -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
@@ -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)
       )
@@ -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)
       )

diff --git a/scripts/run_deepvariant.py b/scripts/run_deepvariant.py
@@ -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
@@ -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):
@@ -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)
       )