diff --git a/Dockerfile b/Dockerfile index 80aa3462..02a14580 100644 --- a/Dockerfile +++ b/Dockerfile @@ -15,7 +15,7 @@ ARG FROM_IMAGE=ubuntu:22.04 # PYTHON_VERSION is also set in settings.sh. ARG PYTHON_VERSION=3.10 ARG DV_GPU_BUILD=0 -ARG VERSION=1.8.0-rc1 +ARG VERSION=1.8.0 ARG TF_ENABLE_ONEDNN_OPTS=1 FROM continuumio/miniconda3 as conda_setup diff --git a/Dockerfile.deepsomatic b/Dockerfile.deepsomatic index 9a3da2fa..70959380 100644 --- a/Dockerfile.deepsomatic +++ b/Dockerfile.deepsomatic @@ -15,7 +15,7 @@ ARG FROM_IMAGE=ubuntu:22.04 # PYTHON_VERSION is also set in settings.sh. ARG PYTHON_VERSION=3.10 ARG DV_GPU_BUILD=0 -ARG VERSION_DEEPSOMATIC=1.7.0 +ARG VERSION_DEEPSOMATIC=1.8.0 ARG TF_ENABLE_ONEDNN_OPTS=1 FROM continuumio/miniconda3 as conda_setup diff --git a/Dockerfile.deeptrio b/Dockerfile.deeptrio index ade759bb..b263df27 100644 --- a/Dockerfile.deeptrio +++ b/Dockerfile.deeptrio @@ -15,7 +15,7 @@ ARG FROM_IMAGE=ubuntu:22.04 # PYTHON_VERSION is also set in settings.sh. ARG PYTHON_VERSION=3.10 ARG DV_GPU_BUILD=0 -ARG VERSION_DEEPTRIO=1.7.0 +ARG VERSION_DEEPTRIO=1.8.0 ARG TF_ENABLE_ONEDNN_OPTS=1 FROM continuumio/miniconda3 as conda_setup diff --git a/Dockerfile.pangenome_aware_deepvariant b/Dockerfile.pangenome_aware_deepvariant index 0f435afc..c9c4a639 100644 --- a/Dockerfile.pangenome_aware_deepvariant +++ b/Dockerfile.pangenome_aware_deepvariant @@ -15,7 +15,7 @@ ARG FROM_IMAGE=ubuntu:22.04 # PYTHON_VERSION is also set in settings.sh. ARG PYTHON_VERSION=3.10 ARG DV_GPU_BUILD=0 -ARG VERSION_DEEPVARIANT=1.7.0 +ARG VERSION_DEEPVARIANT=1.8.0 ARG TF_ENABLE_ONEDNN_OPTS=1 FROM continuumio/miniconda3 AS conda_setup @@ -116,18 +116,24 @@ RUN \ /opt/deepvariant/bin/load_gbz_into_shared_memory \ /opt/deepvariant/bin/run_pangenome_aware_deepvariant -# Copy models. -WORKDIR /opt/models/pangenome_aware_deepvariant/wgs -ADD https://storage.googleapis.com/brain-genomics/pichuan/share/deepvariant/models/PangenomeAwareDeepVariant/${VERSION_DEEPVARIANT}/wgs/weights-111-0.995872.ckpt.data-00000-of-00001 . -ADD https://storage.googleapis.com/brain-genomics/pichuan/share/deepvariant/models/PangenomeAwareDeepVariant/${VERSION_DEEPVARIANT}/wgs/weights-111-0.995872.ckpt.index . -ADD https://storage.googleapis.com/brain-genomics/pichuan/share/deepvariant/models/PangenomeAwareDeepVariant/${VERSION_DEEPVARIANT}/wgs/example_info.json . -RUN chmod -R +r /opt/models/pangenome_aware_deepvariant/wgs/* - -WORKDIR /opt/models/pangenome_aware_deepvariant/wes -ADD https://storage.googleapis.com/brain-genomics/pichuan/share/deepvariant/models/PangenomeAwareDeepVariant/${VERSION_DEEPVARIANT}/wes/weights-31-0.987898.ckpt.data-00000-of-00001 . -ADD https://storage.googleapis.com/brain-genomics/pichuan/share/deepvariant/models/PangenomeAwareDeepVariant/${VERSION_DEEPVARIANT}/wes/weights-31-0.987898.ckpt.index . -ADD https://storage.googleapis.com/brain-genomics/pichuan/share/deepvariant/models/PangenomeAwareDeepVariant/${VERSION_DEEPVARIANT}/wes/example_info.json . -RUN chmod -R +r /opt/models/pangenome_aware_deepvariant/wes/* +# Copy models +WORKDIR opt/models/pangenome_aware_deepvariant/wgs +ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wgs.pagenome.savedmodel/fingerprint.pb . +ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wgs.pagenome.savedmodel/saved_model.pb . +ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wgs.pagenome.savedmodel/example_info.json . +WORKDIR opt/models/pangenome_aware_deepvariant/wgs/variables +ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wgs.pagenome.savedmodel/variables/variables.data-00000-of-00001 . +ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wgs.pagenome.savedmodel/variables/variables.index . +RUN chmod -R +r opt/models/pangenome_aware_deepvariant/wgs/* + +WORKDIR opt/models/pangenome_aware_deepvariant/wes +ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wes.pagenome.savedmodel/fingerprint.pb . +ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wes.pagenome.savedmodel/saved_model.pb . +ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wes.pagenome.savedmodel/example_info.json . +WORKDIR opt/models/pangenome_aware_deepvariant/wes/variables +ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wes.pagenome.savedmodel/variables/variables.data-00000-of-00001 . +ADD https://storage.googleapis.com/deepvariant/models/DeepVariant/${VERSION_DEEPVARIANT}/pangenome_aware_models/savedmodels/deepvariant.wes.pagenome.savedmodel/variables/variables.index . +RUN chmod -R +r opt/models/pangenome_aware_deepvariant/wes/* ENV PATH="${PATH}":/opt/conda/bin:/opt/conda/envs/bio/bin:/opt/deepvariant/bin/pangenome_aware_deepvariant:/opt/deepvariant/bin diff --git a/deeptrio/testdata/HG002_ONT_deeptrio.denovo.examples.tfrecord.gz.example_info.json b/deeptrio/testdata/HG002_ONT_deeptrio.denovo.examples.tfrecord.gz.example_info.json index 5ce7ef63..37896650 100644 --- a/deeptrio/testdata/HG002_ONT_deeptrio.denovo.examples.tfrecord.gz.example_info.json +++ b/deeptrio/testdata/HG002_ONT_deeptrio.denovo.examples.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [300, 199, 9], "channels": [1, 2, 3, 4, 5, 6, 7, 9, 10]} \ No newline at end of file +{"version": "1.8.0", "shape": [300, 199, 9], "channels": [1, 2, 3, 4, 5, 6, 7, 9, 10]} \ No newline at end of file diff --git a/deeptrio/testdata/HG002_ONT_deeptrio.examples.tfrecord.gz.example_info.json b/deeptrio/testdata/HG002_ONT_deeptrio.examples.tfrecord.gz.example_info.json index 5ce7ef63..37896650 100644 --- a/deeptrio/testdata/HG002_ONT_deeptrio.examples.tfrecord.gz.example_info.json +++ b/deeptrio/testdata/HG002_ONT_deeptrio.examples.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [300, 199, 9], "channels": [1, 2, 3, 4, 5, 6, 7, 9, 10]} \ No newline at end of file +{"version": "1.8.0", "shape": [300, 199, 9], "channels": [1, 2, 3, 4, 5, 6, 7, 9, 10]} \ No newline at end of file diff --git a/deeptrio/testdata/alt_aligned_pileup.golden.training_examples.tfrecord.gz.example_info.json b/deeptrio/testdata/alt_aligned_pileup.golden.training_examples.tfrecord.gz.example_info.json index 8021e569..c0a392e4 100644 --- a/deeptrio/testdata/alt_aligned_pileup.golden.training_examples.tfrecord.gz.example_info.json +++ b/deeptrio/testdata/alt_aligned_pileup.golden.training_examples.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [140, 199, 8], "channels": [1, 2, 3, 4, 5, 6, 9, 10]} \ No newline at end of file +{"version": "1.8.0", "shape": [140, 199, 8], "channels": [1, 2, 3, 4, 5, 6, 9, 10]} \ No newline at end of file diff --git a/deeptrio/testdata/customized_classes.golden.training_examples.tfrecord.gz.example_info.json b/deeptrio/testdata/customized_classes.golden.training_examples.tfrecord.gz.example_info.json index e57a09fd..5a4fa554 100644 --- a/deeptrio/testdata/customized_classes.golden.training_examples.tfrecord.gz.example_info.json +++ b/deeptrio/testdata/customized_classes.golden.training_examples.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deeptrio/testdata/golden.calling_examples.tfrecord.gz-00000-of-00003.example_info.json b/deeptrio/testdata/golden.calling_examples.tfrecord.gz-00000-of-00003.example_info.json index e57a09fd..5a4fa554 100644 --- a/deeptrio/testdata/golden.calling_examples.tfrecord.gz-00000-of-00003.example_info.json +++ b/deeptrio/testdata/golden.calling_examples.tfrecord.gz-00000-of-00003.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deeptrio/testdata/golden.calling_examples.tfrecord.gz-00001-of-00003.example_info.json b/deeptrio/testdata/golden.calling_examples.tfrecord.gz-00001-of-00003.example_info.json index e57a09fd..5a4fa554 100644 --- a/deeptrio/testdata/golden.calling_examples.tfrecord.gz-00001-of-00003.example_info.json +++ b/deeptrio/testdata/golden.calling_examples.tfrecord.gz-00001-of-00003.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deeptrio/testdata/golden.calling_examples.tfrecord.gz-00002-of-00003.example_info.json b/deeptrio/testdata/golden.calling_examples.tfrecord.gz-00002-of-00003.example_info.json index e57a09fd..5a4fa554 100644 --- a/deeptrio/testdata/golden.calling_examples.tfrecord.gz-00002-of-00003.example_info.json +++ b/deeptrio/testdata/golden.calling_examples.tfrecord.gz-00002-of-00003.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deeptrio/testdata/golden.calling_examples.tfrecord.gz.example_info.json b/deeptrio/testdata/golden.calling_examples.tfrecord.gz.example_info.json index e57a09fd..5a4fa554 100644 --- a/deeptrio/testdata/golden.calling_examples.tfrecord.gz.example_info.json +++ b/deeptrio/testdata/golden.calling_examples.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deeptrio/testdata/golden.postprocess_gvcf_output.g.vcf b/deeptrio/testdata/golden.postprocess_gvcf_output.g.vcf index 6127cc2d..eb061f5e 100644 --- a/deeptrio/testdata/golden.postprocess_gvcf_output.g.vcf +++ b/deeptrio/testdata/golden.postprocess_gvcf_output.g.vcf @@ -12,7 +12,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##DeepVariant_version=1.7.0 +##DeepVariant_version=1.8.0 ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT child 20 10000000 . T <*> 0 . END=10000011 GT:GQ:MIN_DP:PL 0/0:48:16:0,48,479 diff --git a/deeptrio/testdata/golden.postprocess_single_site_output.vcf b/deeptrio/testdata/golden.postprocess_single_site_output.vcf index 281174d2..8d785b05 100644 --- a/deeptrio/testdata/golden.postprocess_single_site_output.vcf +++ b/deeptrio/testdata/golden.postprocess_single_site_output.vcf @@ -12,7 +12,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##DeepVariant_version=1.7.0 +##DeepVariant_version=1.8.0 ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT child 20 10000117 . C T 13.1 PASS . GT:GQ:DP:AD:VAF:PL 0/1:12:18:6,12:0.666667:12,0,20 diff --git a/deeptrio/testdata/golden.training_examples.tfrecord.gz-00000-of-00003.example_info.json b/deeptrio/testdata/golden.training_examples.tfrecord.gz-00000-of-00003.example_info.json index e57a09fd..5a4fa554 100644 --- a/deeptrio/testdata/golden.training_examples.tfrecord.gz-00000-of-00003.example_info.json +++ b/deeptrio/testdata/golden.training_examples.tfrecord.gz-00000-of-00003.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deeptrio/testdata/golden.training_examples.tfrecord.gz-00001-of-00003.example_info.json b/deeptrio/testdata/golden.training_examples.tfrecord.gz-00001-of-00003.example_info.json index e57a09fd..5a4fa554 100644 --- a/deeptrio/testdata/golden.training_examples.tfrecord.gz-00001-of-00003.example_info.json +++ b/deeptrio/testdata/golden.training_examples.tfrecord.gz-00001-of-00003.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deeptrio/testdata/golden.training_examples.tfrecord.gz-00002-of-00003.example_info.json b/deeptrio/testdata/golden.training_examples.tfrecord.gz-00002-of-00003.example_info.json index e57a09fd..5a4fa554 100644 --- a/deeptrio/testdata/golden.training_examples.tfrecord.gz-00002-of-00003.example_info.json +++ b/deeptrio/testdata/golden.training_examples.tfrecord.gz-00002-of-00003.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deeptrio/testdata/golden.training_examples.tfrecord.gz.example_info.json b/deeptrio/testdata/golden.training_examples.tfrecord.gz.example_info.json index e57a09fd..5a4fa554 100644 --- a/deeptrio/testdata/golden.training_examples.tfrecord.gz.example_info.json +++ b/deeptrio/testdata/golden.training_examples.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deeptrio/testdata/golden.training_examples.vcf b/deeptrio/testdata/golden.training_examples.vcf index 5707c2ae..3a6e4b2e 100644 --- a/deeptrio/testdata/golden.training_examples.vcf +++ b/deeptrio/testdata/golden.training_examples.vcf @@ -12,7 +12,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##DeepVariant_version=1.7.0 +##DeepVariant_version=1.8.0 ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT child 20 10001019 . T G 0 . . GT:DP:AD:VAF 0/1:16:10,6:0.375 diff --git a/deeptrio/testdata/golden.vcf_candidate_importer.calling_examples.tfrecord.gz.example_info.json b/deeptrio/testdata/golden.vcf_candidate_importer.calling_examples.tfrecord.gz.example_info.json index 8373962e..05bb4ae5 100644 --- a/deeptrio/testdata/golden.vcf_candidate_importer.calling_examples.tfrecord.gz.example_info.json +++ b/deeptrio/testdata/golden.vcf_candidate_importer.calling_examples.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [140, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [140, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deeptrio/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz.example_info.json b/deeptrio/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz.example_info.json index 8373962e..05bb4ae5 100644 --- a/deeptrio/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz.example_info.json +++ b/deeptrio/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [140, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [140, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deepvariant/dv_vcf_constants.py b/deepvariant/dv_vcf_constants.py index 1d8b0972..2a8764a3 100644 --- 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 = '1.7.0' +DEEP_VARIANT_VERSION = '1.8.0' # FILTER field IDs. DEEP_VARIANT_PASS = 'PASS' diff --git a/deepvariant/testdata/customized_classes.golden.training_examples.tfrecord.gz b/deepvariant/testdata/customized_classes.golden.training_examples.tfrecord.gz index 3786b1fa..4d24be72 100644 Binary files a/deepvariant/testdata/customized_classes.golden.training_examples.tfrecord.gz and b/deepvariant/testdata/customized_classes.golden.training_examples.tfrecord.gz differ diff --git a/deepvariant/testdata/customized_classes.golden.training_examples.tfrecord.gz.example_info.json b/deepvariant/testdata/customized_classes.golden.training_examples.tfrecord.gz.example_info.json index 3ca51508..54798542 100644 --- a/deepvariant/testdata/customized_classes.golden.training_examples.tfrecord.gz.example_info.json +++ b/deepvariant/testdata/customized_classes.golden.training_examples.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.allele_frequency_examples.tfrecord.gz b/deepvariant/testdata/golden.allele_frequency_examples.tfrecord.gz index df13b118..9dda7277 100644 Binary files a/deepvariant/testdata/golden.allele_frequency_examples.tfrecord.gz and b/deepvariant/testdata/golden.allele_frequency_examples.tfrecord.gz differ 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 index 5d925e04..0670aab8 100644 --- 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": "1.7.0", "shape": [100, 221, 8], "channels": [1, 2, 3, 4, 5, 6, 19, 8]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 8], "channels": [1, 2, 3, 4, 5, 6, 19, 8]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.alt_aligned_pileup_diff_channels_examples.tfrecord.gz b/deepvariant/testdata/golden.alt_aligned_pileup_diff_channels_examples.tfrecord.gz index d7344341..4dc6519b 100644 Binary files a/deepvariant/testdata/golden.alt_aligned_pileup_diff_channels_examples.tfrecord.gz and b/deepvariant/testdata/golden.alt_aligned_pileup_diff_channels_examples.tfrecord.gz differ diff --git a/deepvariant/testdata/golden.alt_aligned_pileup_diff_channels_examples.tfrecord.gz.example_info.json b/deepvariant/testdata/golden.alt_aligned_pileup_diff_channels_examples.tfrecord.gz.example_info.json index 0427549f..7e8d2a6c 100644 --- a/deepvariant/testdata/golden.alt_aligned_pileup_diff_channels_examples.tfrecord.gz.example_info.json +++ b/deepvariant/testdata/golden.alt_aligned_pileup_diff_channels_examples.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [100, 221, 8], "channels": [1, 2, 3, 4, 5, 6, 9, 10]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 8], "channels": [1, 2, 3, 4, 5, 6, 9, 10]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.alt_aligned_pileup_rows_examples.tfrecord.gz b/deepvariant/testdata/golden.alt_aligned_pileup_rows_examples.tfrecord.gz index c82d0c28..e8409574 100644 Binary files a/deepvariant/testdata/golden.alt_aligned_pileup_rows_examples.tfrecord.gz and b/deepvariant/testdata/golden.alt_aligned_pileup_rows_examples.tfrecord.gz differ 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 index 570989dc..774407dd 100644 --- 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": "1.7.0", "shape": [300, 221, 6], "channels": [1, 2, 3, 4, 5, 6]} \ No newline at end of file +{"version": "1.8.0", "shape": [300, 221, 6], "channels": [1, 2, 3, 4, 5, 6]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.calling_candidates.tfrecord.gz b/deepvariant/testdata/golden.calling_candidates.tfrecord.gz index 136f8fcf..ce0dd68e 100644 Binary files a/deepvariant/testdata/golden.calling_candidates.tfrecord.gz and b/deepvariant/testdata/golden.calling_candidates.tfrecord.gz differ diff --git a/deepvariant/testdata/golden.calling_examples.tfrecord.gz b/deepvariant/testdata/golden.calling_examples.tfrecord.gz index c8962778..abdeb109 100644 Binary files a/deepvariant/testdata/golden.calling_examples.tfrecord.gz and b/deepvariant/testdata/golden.calling_examples.tfrecord.gz differ diff --git a/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00000-of-00003 b/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00000-of-00003 index 2b339574..0b371633 100644 Binary files a/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00000-of-00003 and b/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00000-of-00003 differ 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 index 3ca51508..54798542 100644 --- 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": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00001-of-00003 b/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00001-of-00003 index 28d856ea..ac24482e 100644 Binary files a/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00001-of-00003 and b/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00001-of-00003 differ 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 index 3ca51508..54798542 100644 --- 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": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00002-of-00003 b/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00002-of-00003 index ed6be112..3cc91638 100644 Binary files a/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00002-of-00003 and b/deepvariant/testdata/golden.calling_examples.tfrecord.gz-00002-of-00003 differ 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 index 3ca51508..54798542 100644 --- 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": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.calling_examples.tfrecord.gz.example_info.json b/deepvariant/testdata/golden.calling_examples.tfrecord.gz.example_info.json index 3ca51508..54798542 100644 --- 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": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.calling_examples.with_flags.tfrecord.gz b/deepvariant/testdata/golden.calling_examples.with_flags.tfrecord.gz index 8f42208a..c51424ab 100644 Binary files a/deepvariant/testdata/golden.calling_examples.with_flags.tfrecord.gz and b/deepvariant/testdata/golden.calling_examples.with_flags.tfrecord.gz differ diff --git a/deepvariant/testdata/golden.calling_examples.with_flags.tfrecord.gz.example_info.json b/deepvariant/testdata/golden.calling_examples.with_flags.tfrecord.gz.example_info.json index 3ca51508..54798542 100644 --- a/deepvariant/testdata/golden.calling_examples.with_flags.tfrecord.gz.example_info.json +++ b/deepvariant/testdata/golden.calling_examples.with_flags.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.haploid_chr20.postprocess_gvcf_output.g.vcf b/deepvariant/testdata/golden.haploid_chr20.postprocess_gvcf_output.g.vcf index 8decc270..27c9e956 100644 --- a/deepvariant/testdata/golden.haploid_chr20.postprocess_gvcf_output.g.vcf +++ b/deepvariant/testdata/golden.haploid_chr20.postprocess_gvcf_output.g.vcf @@ -12,7 +12,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##DeepVariant_version=1.7.0 +##DeepVariant_version=1.8.0 ##contig= #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.haploid_chr20.postprocess_single_site_output.vcf b/deepvariant/testdata/golden.haploid_chr20.postprocess_single_site_output.vcf index 4d55897a..6963cfe2 100644 --- a/deepvariant/testdata/golden.haploid_chr20.postprocess_single_site_output.vcf +++ b/deepvariant/testdata/golden.haploid_chr20.postprocess_single_site_output.vcf @@ -12,7 +12,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##DeepVariant_version=1.7.0 +##DeepVariant_version=1.8.0 ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 chr20 10000117 . C T 1.2 RefCall . GT:GQ:DP:AD:VAF:PL ./.:6:55:25,30:0.545455:0,97,5 diff --git a/deepvariant/testdata/golden.pacbio_examples.tfrecord.gz.example_info.json b/deepvariant/testdata/golden.pacbio_examples.tfrecord.gz.example_info.json index 864023d3..a0ae1a00 100644 --- a/deepvariant/testdata/golden.pacbio_examples.tfrecord.gz.example_info.json +++ b/deepvariant/testdata/golden.pacbio_examples.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [100, 199, 9], "channels": [1, 2, 3, 4, 5, 6, 7, 9, 10]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 199, 9], "channels": [1, 2, 3, 4, 5, 6, 7, 9, 10]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.postprocess_empty_output.vcf.gz b/deepvariant/testdata/golden.postprocess_empty_output.vcf.gz index 77e69406..e0139476 100644 Binary files a/deepvariant/testdata/golden.postprocess_empty_output.vcf.gz and b/deepvariant/testdata/golden.postprocess_empty_output.vcf.gz differ diff --git a/deepvariant/testdata/golden.postprocess_gvcf_output.g.vcf b/deepvariant/testdata/golden.postprocess_gvcf_output.g.vcf index e6b891b9..453bd484 100644 --- a/deepvariant/testdata/golden.postprocess_gvcf_output.g.vcf +++ b/deepvariant/testdata/golden.postprocess_gvcf_output.g.vcf @@ -12,7 +12,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##DeepVariant_version=1.7.0 +##DeepVariant_version=1.8.0 ##contig= #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 index e1ef9cb4..d30a23ac 100644 --- 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= ##FORMAT= ##FORMAT= -##DeepVariant_version=1.7.0 +##DeepVariant_version=1.8.0 ##contig= #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_input-00000-of-00001.tfrecord.gz b/deepvariant/testdata/golden.postprocess_single_site_input-00000-of-00001.tfrecord.gz index 155afd46..fe03f042 100644 Binary files a/deepvariant/testdata/golden.postprocess_single_site_input-00000-of-00001.tfrecord.gz and b/deepvariant/testdata/golden.postprocess_single_site_input-00000-of-00001.tfrecord.gz differ diff --git a/deepvariant/testdata/golden.postprocess_single_site_output.pass_only.vcf b/deepvariant/testdata/golden.postprocess_single_site_output.pass_only.vcf index 3331afbd..678d5e02 100644 --- 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= ##FORMAT= ##FORMAT= -##DeepVariant_version=1.7.0 +##DeepVariant_version=1.8.0 ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 chr20 10000117 . C T 37.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:36:55:25,30:0.545455:37,0,42 diff --git a/deepvariant/testdata/golden.postprocess_single_site_output.vcf b/deepvariant/testdata/golden.postprocess_single_site_output.vcf index e15c91fe..841cbb22 100644 --- a/deepvariant/testdata/golden.postprocess_single_site_output.vcf +++ b/deepvariant/testdata/golden.postprocess_single_site_output.vcf @@ -12,7 +12,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##DeepVariant_version=1.7.0 +##DeepVariant_version=1.8.0 ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 chr20 10000117 . C T 37.6 PASS . GT:GQ:DP:AD:VAF:PL 0/1:36:55:25,30:0.545455:37,0,42 diff --git a/deepvariant/testdata/golden.postprocess_single_site_output.vcf.gz b/deepvariant/testdata/golden.postprocess_single_site_output.vcf.gz index 89732f8e..57b4ebb5 100644 Binary files a/deepvariant/testdata/golden.postprocess_single_site_output.vcf.gz and b/deepvariant/testdata/golden.postprocess_single_site_output.vcf.gz differ diff --git a/deepvariant/testdata/golden.postprocess_single_site_output_with_small_model.vcf.gz b/deepvariant/testdata/golden.postprocess_single_site_output_with_small_model.vcf.gz index 634eeae5..f9f8db9e 100644 Binary files a/deepvariant/testdata/golden.postprocess_single_site_output_with_small_model.vcf.gz and b/deepvariant/testdata/golden.postprocess_single_site_output_with_small_model.vcf.gz differ diff --git a/deepvariant/testdata/golden.sv_calling_examples.tfrecord.gz b/deepvariant/testdata/golden.sv_calling_examples.tfrecord.gz index 42efb529..1522cf14 100644 Binary files a/deepvariant/testdata/golden.sv_calling_examples.tfrecord.gz and b/deepvariant/testdata/golden.sv_calling_examples.tfrecord.gz differ 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 index cee6c163..6dff9360 100644 --- 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": "1.7.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 7]} \ No newline at end of file +{"version": "1.8.0", "shape": [300, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 7]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.training_examples.tfrecord b/deepvariant/testdata/golden.training_examples.tfrecord index e8de0231..f708f02f 100644 Binary files a/deepvariant/testdata/golden.training_examples.tfrecord and b/deepvariant/testdata/golden.training_examples.tfrecord differ diff --git a/deepvariant/testdata/golden.training_examples.tfrecord.gz b/deepvariant/testdata/golden.training_examples.tfrecord.gz index 2a301cff..bfcc1c05 100644 Binary files a/deepvariant/testdata/golden.training_examples.tfrecord.gz and b/deepvariant/testdata/golden.training_examples.tfrecord.gz differ diff --git a/deepvariant/testdata/golden.training_examples.tfrecord.gz-00000-of-00003 b/deepvariant/testdata/golden.training_examples.tfrecord.gz-00000-of-00003 index 8521fe13..ce06af0e 100644 Binary files a/deepvariant/testdata/golden.training_examples.tfrecord.gz-00000-of-00003 and b/deepvariant/testdata/golden.training_examples.tfrecord.gz-00000-of-00003 differ 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 index 3ca51508..54798542 100644 --- 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": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.training_examples.tfrecord.gz-00001-of-00003 b/deepvariant/testdata/golden.training_examples.tfrecord.gz-00001-of-00003 index a34f36dc..317a4a87 100644 Binary files a/deepvariant/testdata/golden.training_examples.tfrecord.gz-00001-of-00003 and b/deepvariant/testdata/golden.training_examples.tfrecord.gz-00001-of-00003 differ 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 index 3ca51508..54798542 100644 --- 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": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.training_examples.tfrecord.gz-00002-of-00003 b/deepvariant/testdata/golden.training_examples.tfrecord.gz-00002-of-00003 index 356b6ddd..3c9e5f14 100644 Binary files a/deepvariant/testdata/golden.training_examples.tfrecord.gz-00002-of-00003 and b/deepvariant/testdata/golden.training_examples.tfrecord.gz-00002-of-00003 differ 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 index 3ca51508..54798542 100644 --- 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": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.training_examples.tfrecord.gz.example_info.json b/deepvariant/testdata/golden.training_examples.tfrecord.gz.example_info.json index 3ca51508..54798542 100644 --- 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": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.training_examples.tfrecord.gz.run_info.pbtxt b/deepvariant/testdata/golden.training_examples.tfrecord.gz.run_info.pbtxt index 58c68a45..a1e8b765 100644 --- a/deepvariant/testdata/golden.training_examples.tfrecord.gz.run_info.pbtxt +++ b/deepvariant/testdata/golden.training_examples.tfrecord.gz.run_info.pbtxt @@ -3566,14 +3566,15 @@ labeling_metrics { } resource_metrics { host_name: "host" - physical_core_count: 12 - cpu_frequency_mhz: 4053.686458333332 - total_memory_mb: 128668 - wall_time_seconds: 1.2084436416625977 - cpu_user_time_seconds: 9.866901 - cpu_system_time_seconds: 6.787293 - memory_peak_rss_mb: 684 - write_bytes: 282624 + physical_core_count: 32 + cpu_frequency_mhz: 2449.9980000000014 + total_memory_mb: 120736 + wall_time_seconds: 1.1024963855743408 + cpu_user_time_seconds: 9.656006 + cpu_system_time_seconds: 6.691356 + memory_peak_rss_mb: 553 + read_bytes: 229376 + write_bytes: 274432 } stats { num_examples: 49 diff --git a/deepvariant/testdata/golden.training_examples.vcf b/deepvariant/testdata/golden.training_examples.vcf index 5def8c00..76678622 100644 --- a/deepvariant/testdata/golden.training_examples.vcf +++ b/deepvariant/testdata/golden.training_examples.vcf @@ -12,7 +12,7 @@ ##FORMAT= ##FORMAT= ##FORMAT= -##DeepVariant_version=1.7.0 +##DeepVariant_version=1.8.0 ##contig= #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/deepvariant/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz b/deepvariant/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz index 734bba64..816980bc 100644 Binary files a/deepvariant/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz and b/deepvariant/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz differ diff --git a/deepvariant/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz.example_info.json b/deepvariant/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz.example_info.json index 3ca51508..54798542 100644 --- a/deepvariant/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz.example_info.json +++ b/deepvariant/testdata/golden.vcf_candidate_importer.training_examples.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.vcf_candidate_importer_calling_examples.tfrecord.gz b/deepvariant/testdata/golden.vcf_candidate_importer_calling_examples.tfrecord.gz index fc03bdf3..a6ffcef1 100644 Binary files a/deepvariant/testdata/golden.vcf_candidate_importer_calling_examples.tfrecord.gz and b/deepvariant/testdata/golden.vcf_candidate_importer_calling_examples.tfrecord.gz differ diff --git a/deepvariant/testdata/golden.vcf_candidate_importer_calling_examples.tfrecord.gz.example_info.json b/deepvariant/testdata/golden.vcf_candidate_importer_calling_examples.tfrecord.gz.example_info.json index 3ca51508..54798542 100644 --- a/deepvariant/testdata/golden.vcf_candidate_importer_calling_examples.tfrecord.gz.example_info.json +++ b/deepvariant/testdata/golden.vcf_candidate_importer_calling_examples.tfrecord.gz.example_info.json @@ -1 +1 @@ -{"version": "1.7.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file +{"version": "1.8.0", "shape": [100, 221, 7], "channels": [1, 2, 3, 4, 5, 6, 19]} \ No newline at end of file diff --git a/deepvariant/testdata/golden.vcf_candidate_importer_postprocess_single_site_input-00000-of-00001.tfrecord.gz b/deepvariant/testdata/golden.vcf_candidate_importer_postprocess_single_site_input-00000-of-00001.tfrecord.gz index 7a568042..e21f55f4 100644 Binary files a/deepvariant/testdata/golden.vcf_candidate_importer_postprocess_single_site_input-00000-of-00001.tfrecord.gz and b/deepvariant/testdata/golden.vcf_candidate_importer_postprocess_single_site_input-00000-of-00001.tfrecord.gz differ 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 index cb88e3e8..35e354e0 100644 --- 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= ##FORMAT= ##FORMAT= -##DeepVariant_version=1.7.0 +##DeepVariant_version=1.8.0 ##contig= #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878 chr20 59777010 . C CCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCACCAGGATCCCCTGTAAGTGTCACCTCCATCCTCACCAGGACCCTCCATGAGTGTCACCTCCATCCTCACTCAGGACCCTCCATGGTGTCACCTCCATCCTCA 0.5 NoCall . GT:GQ:DP:AD:VAF:PL ./.:0:0:0,0:0:0,0 diff --git a/docs/visualizing_examples.ipynb b/docs/visualizing_examples.ipynb index 8920afb1..567940ec 100644 --- a/docs/visualizing_examples.ipynb +++ b/docs/visualizing_examples.ipynb @@ -35,10 +35,10 @@ "source": [ "\n", " \n", " \n", "
\n", - " Run in Google Colab\n", + " Run in Google Colab\n", " \n", - " View source on GitHub\n", + " View source on GitHub\n", "
" ] diff --git a/scripts/run_deepsomatic.py b/scripts/run_deepsomatic.py index e504977f..6c5f51f1 100644 --- a/scripts/run_deepsomatic.py +++ b/scripts/run_deepsomatic.py @@ -286,7 +286,7 @@ # Current release version of DeepVariant. # Should be the same in dv_vcf_constants.py. -DEEP_VARIANT_VERSION = '1.7.0' +DEEP_VARIANT_VERSION = '1.8.0' @enum.unique @@ -751,7 +751,7 @@ def check_flags(): raise RuntimeError( 'The model files {}* do not exist. Potentially ' 'relevant issue: ' - 'https://github.com/google/deepvariant/blob/r1.7/docs/' + 'https://github.com/google/deepvariant/blob/r1.8/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 index 5c51c787..8a4564f0 100644 --- a/scripts/run_deeptrio.py +++ b/scripts/run_deeptrio.py @@ -310,7 +310,7 @@ # Current release version of DeepTrio. # Should be the same in dv_vcf_constants.py. -DEEP_TRIO_VERSION = '1.7.0' +DEEP_TRIO_VERSION = '1.8.0' GLNEXUS_VERSION = 'v1.2.7' DEEP_TRIO_WGS_PILEUP_HEIGHT_CHILD = 60 @@ -759,7 +759,7 @@ def check_flags(): raise RuntimeError( 'The model files {}* do not exist. Potentially ' 'relevant issue: ' - 'https://github.com/google/deepvariant/blob/r1.7/docs/' + 'https://github.com/google/deepvariant/blob/r1.8/docs/' 'FAQ.md#why-cant-it-find-one-of-the-input-files-eg-' 'could-not-open'.format(_CUSTOMIZED_MODEL_PARENT.value) ) @@ -778,7 +778,7 @@ def check_flags(): raise RuntimeError( 'The model files {}* do not exist. Potentially ' 'relevant issue: ' - 'https://github.com/google/deepvariant/blob/r1.7/docs/' + 'https://github.com/google/deepvariant/blob/r1.8/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 index 753fd3f1..7f11a285 100644 --- 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/r1.7/docs/deepvariant-quick-start.md +https://github.com/google/deepvariant/blob/r1.8/docs/deepvariant-quick-start.md """ import dataclasses @@ -317,7 +317,7 @@ class SmallModelConfig: # Current release version of DeepVariant. # Should be the same in dv_vcf_constants.py. -DEEP_VARIANT_VERSION = '1.7.0' +DEEP_VARIANT_VERSION = '1.8.0' def _is_quoted(value): @@ -654,7 +654,7 @@ def check_flags(): raise RuntimeError( 'The model files {}* do not exist. Potentially ' 'relevant issue: ' - 'https://github.com/google/deepvariant/blob/r1.7/docs/' + 'https://github.com/google/deepvariant/blob/r1.8/docs/' 'FAQ.md#why-cant-it-find-one-of-the-input-files-eg-' 'could-not-open'.format(_CUSTOMIZED_MODEL.value) )