{"payload":{"feedbackUrl":"https://github.com/orgs/community/discussions/53140","repo":{"id":111751293,"defaultBranch":"r1.6.1","name":"deepvariant","ownerLogin":"google","currentUserCanPush":false,"isFork":false,"isEmpty":false,"createdAt":"2017-11-23T01:56:22.000Z","ownerAvatar":"https://avatars.githubusercontent.com/u/1342004?v=4","public":true,"private":false,"isOrgOwned":true},"refInfo":{"name":"","listCacheKey":"v0:1710876010.0","currentOid":""},"activityList":{"items":[{"before":null,"after":"bf9ed7e6de97cf6c8381694cb996317a740625ad","ref":"refs/heads/r1.6.1","pushedAt":"2024-03-18T21:04:16.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Resolve conflicts in test files","shortMessageHtmlLink":"Resolve conflicts in test files"}},{"before":"2202aad21b4828932e1756be6ea7164dbe1f2989","after":"c7725599e0634f19207311b588a2b6fadb8e04b5","ref":"refs/heads/dev","pushedAt":"2024-01-26T20:28:01.000Z","pushType":"push","commitsCount":63,"pusher":{"login":"pichuan","name":"Pi-Chuan Chang","path":"/pichuan","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/471813?s=80&v=4"},"commit":{"message":"Modify BuildPileupForOneSample() signature.\n\nPiperOrigin-RevId: 601514831","shortMessageHtmlLink":"Modify BuildPileupForOneSample() signature."}},{"before":"764bad20cbfa178d757ae81bbe05860640f2d5d4","after":"73a8046d2368393ab2f20125bc3b7b39e71935d1","ref":"refs/heads/r1.6","pushedAt":"2023-12-09T00:22:24.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"pichuan","name":"Pi-Chuan Chang","path":"/pichuan","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/471813?s=80&v=4"},"commit":{"message":"Update problem_report.md","shortMessageHtmlLink":"Update problem_report.md"}},{"before":"360ee6fc7921caf219b424cddf2d9a3d09830b5c","after":"2202aad21b4828932e1756be6ea7164dbe1f2989","ref":"refs/heads/dev","pushedAt":"2023-11-02T19:18:07.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Update readme to fix link.\n\nPiperOrigin-RevId: 578937926","shortMessageHtmlLink":"Update readme to fix link."}},{"before":"68ff45a82f768268bc981f101ec713049f676607","after":"764bad20cbfa178d757ae81bbe05860640f2d5d4","ref":"refs/heads/r1.6","pushedAt":"2023-11-02T19:17:09.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Update readme to fix link.\n\nPiperOrigin-RevId: 578937926","shortMessageHtmlLink":"Update readme to fix link."}},{"before":"68ff45a82f768268bc981f101ec713049f676607","after":"764bad20cbfa178d757ae81bbe05860640f2d5d4","ref":"refs/heads/master","pushedAt":"2023-11-02T19:16:56.000Z","pushType":"push","commitsCount":1,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Update readme to fix link.\n\nPiperOrigin-RevId: 578937926","shortMessageHtmlLink":"Update readme to fix link."}},{"before":"ed458a0b4cab8085b6036df9020f566817779704","after":"360ee6fc7921caf219b424cddf2d9a3d09830b5c","ref":"refs/heads/dev","pushedAt":"2023-11-02T19:02:33.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Update VG documentation.\n\nPiperOrigin-RevId: 578889599","shortMessageHtmlLink":"Update VG documentation."}},{"before":"6b167016a0e6b92ca5b492e2dac9000d97c8d3ee","after":"68ff45a82f768268bc981f101ec713049f676607","ref":"refs/heads/r1.6","pushedAt":"2023-11-02T19:01:15.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Update VG documentation.\n\nPiperOrigin-RevId: 578889599","shortMessageHtmlLink":"Update VG documentation."}},{"before":"6b167016a0e6b92ca5b492e2dac9000d97c8d3ee","after":"68ff45a82f768268bc981f101ec713049f676607","ref":"refs/heads/master","pushedAt":"2023-11-02T19:00:50.000Z","pushType":"push","commitsCount":4,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Update VG documentation.\n\nPiperOrigin-RevId: 578889599","shortMessageHtmlLink":"Update VG documentation."}},{"before":null,"after":"6b167016a0e6b92ca5b492e2dac9000d97c8d3ee","ref":"refs/heads/r1.6","pushedAt":"2023-10-23T19:39:19.000Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Add logic to run_deepvariant to control postprocess cpus\n\nPiperOrigin-RevId: 575883359","shortMessageHtmlLink":"Add logic to run_deepvariant to control postprocess cpus"}},{"before":"806d82c8f8c56b8310c736082ebe984427dc7d38","after":"ed458a0b4cab8085b6036df9020f566817779704","ref":"refs/heads/dev","pushedAt":"2023-10-23T19:33:04.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Add logic to run_deepvariant to control postprocess cpus\n\nPiperOrigin-RevId: 575883359","shortMessageHtmlLink":"Add logic to run_deepvariant to control postprocess cpus"}},{"before":"9e5b8e25cbae50018895997ebd811f0f3ce2fb10","after":"6b167016a0e6b92ca5b492e2dac9000d97c8d3ee","ref":"refs/heads/master","pushedAt":"2023-10-23T19:30:35.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Add logic to run_deepvariant to control postprocess cpus\n\nPiperOrigin-RevId: 575883359","shortMessageHtmlLink":"Add logic to run_deepvariant to control postprocess cpus"}},{"before":"3e22456b4300b3ba98bfdd71819c3d002faece79","after":"806d82c8f8c56b8310c736082ebe984427dc7d38","ref":"refs/heads/dev","pushedAt":"2023-10-20T23:51:31.000Z","pushType":"push","commitsCount":13,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Update FAQ files\n\nPiperOrigin-RevId: 575340197","shortMessageHtmlLink":"Update FAQ files"}},{"before":"07451e14dbc94320b860b1fa30d62e93bcaa3b09","after":"9e5b8e25cbae50018895997ebd811f0f3ce2fb10","ref":"refs/heads/master","pushedAt":"2023-10-20T23:49:17.000Z","pushType":"push","commitsCount":13,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Update FAQ files\n\nPiperOrigin-RevId: 575340197","shortMessageHtmlLink":"Update FAQ files"}},{"before":"b12cadde4b1b70f2b447568bccf9e51bc73f9ec4","after":"3e22456b4300b3ba98bfdd71819c3d002faece79","ref":"refs/heads/dev","pushedAt":"2023-10-18T06:14:57.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Change shape consistency logic.\n\nPiperOrigin-RevId: 574351624","shortMessageHtmlLink":"Change shape consistency logic."}},{"before":"2ca2d9f396fabca74aa1012a4a6832d84cb22b4e","after":"07451e14dbc94320b860b1fa30d62e93bcaa3b09","ref":"refs/heads/master","pushedAt":"2023-10-18T06:09:00.000Z","pushType":"push","commitsCount":2,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Change shape consistency logic.\n\nPiperOrigin-RevId: 574351624","shortMessageHtmlLink":"Change shape consistency logic."}},{"before":"95ec8de822d5540e40532c0716e3be8fc0d39777","after":"b12cadde4b1b70f2b447568bccf9e51bc73f9ec4","ref":"refs/heads/dev","pushedAt":"2023-10-17T18:25:18.000Z","pushType":"push","commitsCount":90,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Update vg version.\n\nPiperOrigin-RevId: 574163419","shortMessageHtmlLink":"Update vg version."}},{"before":"ab068c4588a02e2167051bd9e74c0c9579462b51","after":"2ca2d9f396fabca74aa1012a4a6832d84cb22b4e","ref":"refs/heads/master","pushedAt":"2023-10-17T18:04:40.000Z","pushType":"push","commitsCount":250,"pusher":{"login":"kishwarshafin","name":"Kishwar Shafin","path":"/kishwarshafin","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/10559039?s=80&v=4"},"commit":{"message":"Update vg version.\n\nPiperOrigin-RevId: 574163419","shortMessageHtmlLink":"Update vg version."}},{"before":"9c6ba8b1b3edd7f7c39293d6cb72a8daae439a7f","after":"95ec8de822d5540e40532c0716e3be8fc0d39777","ref":"refs/heads/dev","pushedAt":"2023-08-11T21:56:51.000Z","pushType":"pr_merge","commitsCount":50,"pusher":{"login":"pichuan","name":"Pi-Chuan Chang","path":"/pichuan","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/471813?s=80&v=4"},"commit":{"message":"Move train_inceptionv3.py to OSS.\n\nPiperOrigin-RevId: 556024308","shortMessageHtmlLink":"Move train_inceptionv3.py to OSS."}},{"before":"ab068c4588a02e2167051bd9e74c0c9579462b51","after":"9c6ba8b1b3edd7f7c39293d6cb72a8daae439a7f","ref":"refs/heads/dev","pushedAt":"2023-06-15T05:09:17.410Z","pushType":"pr_merge","commitsCount":110,"pusher":{"login":"pichuan","name":"Pi-Chuan Chang","path":"/pichuan","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/471813?s=80&v=4"},"commit":{"message":"Fix the edge case in align_to_all_haplotypes.\n\nPiperOrigin-RevId: 540412059","shortMessageHtmlLink":"Fix the edge case in align_to_all_haplotypes."}},{"before":null,"after":"ab068c4588a02e2167051bd9e74c0c9579462b51","ref":"refs/heads/dev","pushedAt":"2023-06-15T05:05:53.354Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"pichuan","name":"Pi-Chuan Chang","path":"/pichuan","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/471813?s=80&v=4"},"commit":{"message":"Update README.md\n\nPiperOrigin-RevId: 512838102","shortMessageHtmlLink":"Update README.md"}},{"before":"0f9258210da05196ce6e3c859e20f318085637fe","after":null,"ref":"refs/heads/dev","pushedAt":"2023-06-15T05:05:34.897Z","pushType":"branch_deletion","commitsCount":0,"pusher":{"login":"pichuan","name":"Pi-Chuan Chang","path":"/pichuan","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/471813?s=80&v=4"}},{"before":"ab068c4588a02e2167051bd9e74c0c9579462b51","after":"0f9258210da05196ce6e3c859e20f318085637fe","ref":"refs/heads/dev","pushedAt":"2023-06-06T16:49:43.692Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"pichuan","name":"Pi-Chuan Chang","path":"/pichuan","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/471813?s=80&v=4"},"commit":{"message":"dev branch (#658)\n\n* Rename the forked IsGoodAltAllele function to IsGoodAltAlleleWithReason.\r\n\r\nPiperOrigin-RevId: 513572461\r\n\r\n* Use `pysam.FastaFile` instead of `nucleus.fasta.FastaReader` in `postprocess_variants`.\r\n\r\nPiperOrigin-RevId: 513621297\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 514019312\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 514027408\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 514032317\r\n\r\n* Replace usage of the tsl::Status constructor with a tsl::{error, errors}::Code.\r\n\r\nPiperOrigin-RevId: 514324857\r\n\r\n* Automated g4 rollback of changelist 514027408\r\n\r\nPiperOrigin-RevId: 514546454\r\n\r\n* Automated g4 rollback of changelist 514019312\r\n\r\nPiperOrigin-RevId: 514554280\r\n\r\n* Add missing include <string>\r\n\r\nPiperOrigin-RevId: 514563281\r\n\r\n* Add a few unit tests for keras_modeling.py.\r\n\r\nPiperOrigin-RevId: 514600640\r\n\r\n* Use parameterized.TestCase. Use dv_constants.NUM_CLASSES.\r\n\r\nPiperOrigin-RevId: 514754831\r\n\r\n* Allow cases when labels are only in INFO for `--labeler_algorithm=customized_classes_labeler`\r\n\r\nPiperOrigin-RevId: 514794174\r\n\r\n* Use gcloud storage cp.\r\n\r\nPiperOrigin-RevId: 515153194\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 515247488\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 515248179\r\n\r\n* Add logic for determining the number of channels from a DeepVariant checkpoint file.\r\n\r\nPiperOrigin-RevId: 515737601\r\n\r\n* Add logic for initializing a DeepVariant model with another DeepVariant model with different number of channels. This can be useful for cases such as initiating from an ImageNet model, which we used to do with Slim models in the past.\r\n\r\nPiperOrigin-RevId: 515752078\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 515830451\r\n\r\n* Update python formatting\r\n\r\nPiperOrigin-RevId: 516024773\r\n\r\n* pyformat `dv_utils_test.py`\r\n\r\nPiperOrigin-RevId: 516219646\r\n\r\n* pyformat `vcf_stats_vis_test.py`\r\n\r\nPiperOrigin-RevId: 516252741\r\n\r\n* Update make_examples_core.py with updated pyformat.\r\n\r\nPiperOrigin-RevId: 516253578\r\n\r\n* Disembiguate the use of the Protobuf, int, and error-code.\r\n\r\n- Use `raw_code()` instead of `code()` when we need an int.\r\n- Cast to the `tensorflow::error::Code`, when setting up a protobuf field, or when calling e.g. the protobuf Code_Name function.\r\n\r\nPiperOrigin-RevId: 516258997\r\n\r\n* pyformat `attention_module.py` and `keras_modeling.py`\r\n\r\nPiperOrigin-RevId: 516263405\r\n\r\n* Update call_variants_test.py formatting.\r\n\r\nPiperOrigin-RevId: 516264270\r\n\r\n* pyformat `model_eval.py`\r\n\r\nPiperOrigin-RevId: 516276732\r\n\r\n* Implement multiprocessing-based inference for keras implementation.\r\n\r\nPiperOrigin-RevId: 516350365\r\n\r\n* Update inference_deepvariant.sh to be able to take --regions from gs://\r\n\r\nPiperOrigin-RevId: 516356865\r\n\r\n* Improve the way epath.Path glob is used, so it works with gs:// paths.\r\n\r\nPiperOrigin-RevId: 516608491\r\n\r\n* pyformat run_deepvariant.py and run_deeptrio.py.\r\n\r\nPiperOrigin-RevId: 516869777\r\n\r\n* Replace usage of the tsl::Status constructor with a tsl::{error, errors}::Code.\r\n\r\nPiperOrigin-RevId: 517894110\r\n\r\n* Remove unused .tfrecord testdata.\r\nEND_PUBLIC\r\n\r\nI reran `learning/genomics/internal/create_golden_deep_trio.sh` to confirm that the file is deleted.\r\n\r\nThe changes look like this:\r\n```\r\nChange 517703340 : BEGIN_PUBLIC Remove unused .tfrecord testdata.\r\n\r\nPiperOrigin-RevId: 518008657\r\n\r\n* Replace all usage of Nucleus tfrecord.Writer with the tf.io.TFRecordWriter directly from TF.\r\n\r\nPiperOrigin-RevId: 518008926\r\n\r\n* Format Python files.\r\n\r\nPiperOrigin-RevId: 518020013\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 518061280\r\n\r\n* Update testdata.\r\n\r\nPiperOrigin-RevId: 518089118\r\n\r\n* pyformat `postprocess_variants_test.py` and `postprocess_variants_pysam_test.py`\r\n\r\nPiperOrigin-RevId: 518371707\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 518964032\r\n\r\n* Update vcf_stats_report entry points and add custom title.\r\n\r\n1. Remove vcf_stats_report from postprocess_variants step. Change run_deepvariant.py and run_deeptrio.py to run that report step separately.\r\n2. Add custom title to VCF stats report for the standalone script and through run_deepvariant.py. For run_deeptrio.py, I did not add an optional title for the report because keeping the sample name seems less error-prone when there are so many flags to set already.\r\n3. Make run_deepvariant.py a binary so it is testable locally with `--dry_run`.\r\n4. Add vcf_stats_report binary to DeepTrio Dockerfile.\r\n\r\nPiperOrigin-RevId: 518969627\r\n\r\n* Automated g4 rollback of changelist 518964032\r\n\r\nPiperOrigin-RevId: 518985605\r\n\r\n* Automated g4 rollback of changelist 511397175\r\n\r\nPiperOrigin-RevId: 519173075\r\n\r\n* Add ONT options to run_case_study_keras\r\n\r\nPiperOrigin-RevId: 519250948\r\n\r\n* Special processing for non_autosomes chromosomes.\r\n\r\nPiperOrigin-RevId: 519275416\r\n\r\n* Post-v1.5 release, allow DeepTrio to use PACBIO mode again.\r\n\r\nPiperOrigin-RevId: 519773700\r\n\r\n* Special processing for non_autosomes chromosomes.\r\n\r\nPiperOrigin-RevId: 519793282\r\n\r\n* Automated g4 rollback of changelist 518008926\r\n\r\nPiperOrigin-RevId: 520041537\r\n\r\n* Add optional phasing info output.\r\n\r\nPiperOrigin-RevId: 520372805\r\n\r\n* [somatic] Add `max_fraction_snps_for_non_target_sample` and `max_fraction_indels_for_non_target_sample` which is used to remove variants that have higher AF from the normal (non-target in the somatic context) sample.\r\n\r\nPiperOrigin-RevId: 520666963\r\n\r\n* Exclude non-DNA regions larger than 300,000 bases.\r\n\r\nPiperOrigin-RevId: 520783371\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 520854857\r\n\r\n* Improve find_ref_n_regions algorithm.\r\n\r\nPiperOrigin-RevId: 520969203\r\n\r\n* Add vsc_max_fraction_{snps,indels}_for_non_target_sample flags.\r\n\r\nPiperOrigin-RevId: 520978138\r\n\r\n* Fix typos.\r\n\r\nPiperOrigin-RevId: 521515484\r\n\r\n* Fix the make_examples_somatic binary. Also adding some default values.\r\n\r\nPiperOrigin-RevId: 521764449\r\n\r\n* Fix the logic of options check in make_examples_somatic.\r\n\r\nPiperOrigin-RevId: 521842184\r\n\r\n* Fork tensorflow::Status to nucleus, to remove the dependency on `tensorflow::Status`.\r\n\r\nPiperOrigin-RevId: 522267964\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 522482285\r\n\r\n* Update call_variants_keras to be more robust - even if the example shape isn't extractable from the json file (e.g., if the json file doesn't exist), we can still extract the shape from the example.\r\n\r\nPiperOrigin-RevId: 522707391\r\n\r\n* Initialize the InceptionV3 backbone model with `imagenet` (instead of using None which means random init).\r\n\r\nIn order to make this work, I had to add extra logic to the Model code to input the shape information earlier.\r\n\r\nNOTE: This was disabled in unit tests, because `imagenet` default will load a model from the internet. Which doesn't work for unit tests.\r\n\r\nPiperOrigin-RevId: 523457598\r\n\r\n* Pass allele_counters by pointer to improve a runtime performance.\r\n\r\nPiperOrigin-RevId: 523465372\r\n\r\n* No need to initialize the inceptionv3 model in call_variants_keras with `imagenet`, because we'll load weights on our own.\r\n\r\nPiperOrigin-RevId: 523734474\r\n\r\n* Fix logic for model initialization in keras.\r\n\r\nPiperOrigin-RevId: 523831973\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 524070859\r\n\r\n* Add a unit test in make_examples_somatic_test.py to illustrate the current situation - in calling mode, the examples are generated with the _normal and _tumor suffixes. We'll want to change this later.\r\n\r\nPiperOrigin-RevId: 524091279\r\n\r\n* Automated g4 rollback of changelist 524070859\r\n\r\nPiperOrigin-RevId: 524116758\r\n\r\n* For make_examples_somatic calling mode, we don't need to generate examples for _normal. `make_examples_somatic` uses multisample code, which previously will always generate examples for each of the sample. In this change, we introduce an option to skip examples and other outputs for specified samples.\r\nAnd, if only one sample is generating output, the code will skip adding the _sample suffix completely.\r\n\r\nPiperOrigin-RevId: 524380775\r\n\r\n* Remove usages of `tsl::Status::error_message`.\r\n\r\nPiperOrigin-RevId: 524512615\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 525031665\r\n\r\n* Roll back a change that breaks the external build.\r\nEND_PUBLIC\r\n\r\nBEGIN_PUBLIC\r\nAutomated g4 rollback of changelist 525031665\r\n\r\nPiperOrigin-RevId: 525202921\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 525394815\r\n\r\n* Point to public case study outputs from the metrics page.\r\n\r\nPiperOrigin-RevId: 525493772\r\n\r\n* Automated g4 rollback of changelist 525394815\r\n\r\nPiperOrigin-RevId: 525504035\r\n\r\n* Implement get_candidate_positions for VcfImporter to allow direct phasing with imported candidates.\r\n\r\nPiperOrigin-RevId: 526135231\r\n\r\n* 1. Remove the --use_candidate_partition check so we can actually run the script.\r\n2. Remove the DT PacBio images from Dockerfile.deeptrio for now because they don't exist.\r\n\r\nPiperOrigin-RevId: 526691111\r\n\r\n* No need to force --use_candidate_partition in inference_deeptrio.sh.\r\n\r\nPiperOrigin-RevId: 526764858\r\n\r\n* Add --discard_non_dna_regions flag to DeepTrio script.\r\n\r\nPiperOrigin-RevId: 526765950\r\n\r\n* Limit reads per region depending on dynamic number of bases covered.\r\n\r\nPiperOrigin-RevId: 527439333\r\n\r\n* Add --java_runtime_version=remotejdk_11.\r\n\r\nPiperOrigin-RevId: 527441201\r\n\r\n* Add --max_reads_for_dynamic_bases_per_region=200 by default\r\nto DeepTrio PacBio.\r\n\r\nPiperOrigin-RevId: 527723098\r\n\r\n* Add X,Y support flags to run_deepvariant\r\n\r\nPiperOrigin-RevId: 528007335\r\n\r\n* Simplify the script: --discard_non_dna_regions can be passed in through make_examples_extra_args.\r\n\r\nPiperOrigin-RevId: 528042876\r\n\r\n* Change the input of the inceptionv3 model, which shouldn't make a difference.\r\n\r\nPiperOrigin-RevId: 528601987\r\n\r\n* Internal Code Change\r\n\r\nPiperOrigin-RevId: 528702795\r\n\r\n* Roll back a change that breaks the external build.\r\nEND_PUBLIC\r\n\r\nBEGIN_PUBLIC\r\nAutomated g4 rollback of changelist 528702795\r\n\r\nPiperOrigin-RevId: 528834401\r\n\r\n* Add a `--output_sitelist` flag to DeepVariant.\r\n\r\nPiperOrigin-RevId: 528879605\r\n\r\n* labeled_examples_to_vcf previously assumes that the Variant inside needs to have GT.\r\nThis change makes it possible to fall back to the `label` field from the tf.Example if the variant doesn't have GT.\r\n\r\nPiperOrigin-RevId: 529446739\r\n\r\n* Improve the way our inceptionv3 model is wired. However, this will make any previously trained model unusable.\r\n\r\nPiperOrigin-RevId: 529470035\r\n\r\n* Make install_singularity.sh executable.\r\n\r\nPiperOrigin-RevId: 529527437\r\n\r\n* Replace usage of Nucleus tfrecord.Writer with tf.io.TFRecordWriter in make_examples_core.\r\n\r\nPiperOrigin-RevId: 530434065\r\n\r\n* Add curation, TSV filtering, and tfrecord output to show_examples.\r\n\r\nPiperOrigin-RevId: 532189184\r\n\r\n* Add run_deepsomatic.py. Note that this is not a feature that we support yet. We have not released a model for this use either.\r\n\r\nPiperOrigin-RevId: 532593108\r\n\r\n* Simplify postprocess_variants_command in run_deepvariant.py.\r\n\r\nPiperOrigin-RevId: 532615106\r\n\r\n* Add run_deepsomatic to Dockerfile.\r\n\r\nPiperOrigin-RevId: 532642395\r\n\r\n* Add a --use_keras_model flag to run_deepsomatic.\r\n\r\nPiperOrigin-RevId: 533182209\r\n\r\n* Update the model check -- Keras model doesn't have the .meta file.\r\n\r\nPiperOrigin-RevId: 533227014\r\n\r\n* Internal change\r\n\r\nPiperOrigin-RevId: 533475534\r\n\r\n* Port base, base quality and base differs from ref channel to OptChannels\r\n\r\nPiperOrigin-RevId: 533528417\r\n\r\n* Update make_examples\r\n\r\nPiperOrigin-RevId: 533606366\r\n\r\n* Add ONT options to DeepSomatic's `run_deepsomatic`\r\n\r\nPiperOrigin-RevId: 534584332\r\n\r\n* Internal Change.\r\n\r\nPiperOrigin-RevId: 535535667\r\n\r\n* Header file for merge_phased_reads implementation.\r\n\r\nPiperOrigin-RevId: 537347042\r\n\r\n* Introduce --use_keras_model flag for run_deepvariant.\r\n\r\nPiperOrigin-RevId: 537464820\r\n\r\n* Use use_keras_model in run_deepvariant.\r\nRemove run_deepvariant_keras because now the same functionality exists in run_deepvariant.\r\n\r\nPiperOrigin-RevId: 537476629\r\n\r\n---------\r\n\r\nCo-authored-by: lucasbrambrink <lucasbrambrink@google.com>\r\nCo-authored-by: Genomics team in Google Health <no-reply@google.com>\r\nCo-authored-by: koles <koles@google.com>\r\nCo-authored-by: danielecook <danielecook@google.com>\r\nCo-authored-by: shafin <shafin@google.com>\r\nCo-authored-by: marianattestad <marianattestad@google.com>\r\nCo-authored-by: jblespiau <jblespiau@google.com>\r\nCo-authored-by: msamman <msamman@google.com>","shortMessageHtmlLink":"dev branch (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1744231617\" data-permission-text=\"Title is private\" data-url=\"https://github.com/google/deepvariant/issues/658\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/google/deepvariant/pull/658/hovercard\" href=\"https://github.com/google/deepvariant/pull/658\">#658</a>)"}},{"before":null,"after":"ab068c4588a02e2167051bd9e74c0c9579462b51","ref":"refs/heads/dev","pushedAt":"2023-06-06T15:31:10.974Z","pushType":"branch_creation","commitsCount":0,"pusher":{"login":"pichuan","name":"Pi-Chuan Chang","path":"/pichuan","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/471813?s=80&v=4"},"commit":{"message":"Update README.md\n\nPiperOrigin-RevId: 512838102","shortMessageHtmlLink":"Update README.md"}},{"before":"5659df3b20d9e5375378855fa20edce48541cc6d","after":"4e03c66f4d2fe0a1ce13374b00955b3543d28e43","ref":"refs/heads/gh-pages","pushedAt":"2023-05-30T21:20:06.800Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"pichuan","name":"Pi-Chuan Chang","path":"/pichuan","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/471813?s=80&v=4"},"commit":{"message":"Adding links to new blog posts. (#654)","shortMessageHtmlLink":"Adding links to new blog posts. (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1733029776\" data-permission-text=\"Title is private\" data-url=\"https://github.com/google/deepvariant/issues/654\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/google/deepvariant/pull/654/hovercard\" href=\"https://github.com/google/deepvariant/pull/654\">#654</a>)"}},{"before":"561358696e1aad95ff55c522b130daa89725a829","after":"5659df3b20d9e5375378855fa20edce48541cc6d","ref":"refs/heads/gh-pages","pushedAt":"2023-03-17T20:09:37.000Z","pushType":"pr_merge","commitsCount":1,"pusher":{"login":"pichuan","name":"Pi-Chuan Chang","path":"/pichuan","primaryAvatarUrl":"https://avatars.githubusercontent.com/u/471813?s=80&v=4"},"commit":{"message":"Add bbviPRS blog post. (#621)\n\n* Preview of bbviPRS blog for testing.\n\n* Adding nickfurlotte to author list along with image.\n\n* Rename 2023-03-20-black-box-variational-inference-for-prs.markdown to 2023-03-16-black-box-variational-inference-for-prs.markdown\n\nChanged date in name.\n\n* change publication date in header.\n\n* Delete current headshot for nickfurlotte.\n\n* Add new headshot for nickfurlottte.\n\n* Initial push of completed bbviPRS blog post and images.\n\n* Add mathjax library to html header.\n\n* Update javascript to add math delimiters.\n\n* Formatting debugging.\n\n* Add author link for nickfurlotte. Update some formatting in post.\n\n* Fix tab in authors.\n\n* Put in links for the colab.\n\n* Few more small fixes.\n\n---------\n\nCo-authored-by: Nick Furlotte <nickfurlotte@google.com>","shortMessageHtmlLink":"Add bbviPRS blog post. (<a class=\"issue-link js-issue-link\" data-error-text=\"Failed to load title\" data-id=\"1629868814\" data-permission-text=\"Title is private\" data-url=\"https://github.com/google/deepvariant/issues/621\" data-hovercard-type=\"pull_request\" data-hovercard-url=\"/google/deepvariant/pull/621/hovercard\" href=\"https://github.com/google/deepvariant/pull/621\">#621</a>)"}}],"hasNextPage":false,"hasPreviousPage":false,"activityType":"all","actor":null,"timePeriod":"all","sort":"DESC","perPage":30,"cursor":"djE6ks8AAAAEGPnq6QA","startCursor":null,"endCursor":null}},"title":"Activity · google/deepvariant"}