These commits are when the Protocol Buffers files have changed: (only the last 100 relevant commits are shown)
| Commit: | d6da5ac | |
|---|---|---|
| Author: | Genomics team in Google Health | |
| Committer: | Copybara-Service | |
Implement methylation-aware phasing support PiperOrigin-RevId: 738436840
| Commit: | 36bce4d | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] Expands the SM code to handle multiple samples. - tracks the `sample_name` in the `DeepVariantCall.ReadSupport` proto. - updates the `small_model_makes_examples` to compute the `BaseFeatures` per sample - update training code/configs to set the above params. PiperOrigin-RevId: 736249896
| Commit: | ed53c6d | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add `--output_debug_info` to control if extra debug info should be output. By default, it's False, to reduce the amount of log info. PiperOrigin-RevId: 735921061
| Commit: | 534ed69 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add non-uniform downsampling flags for DeepSomatic. PiperOrigin-RevId: 734640273
| Commit: | 4a01e8e | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Change window_selector logic. PiperOrigin-RevId: 734309163
| Commit: | f605fa7 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Add 6mA channel. PiperOrigin-RevId: 734230252
| Commit: | 5bf1d7f | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] Refactors how small model is instantiated in `make_examples`. This ties the variant caller to the `sample_lib.Sample`, similar to how each sample has its own reader. - moves `trained_small_model_path` to `make_examples.py` for each binary (currently DV and Pangenome-DV). - this is a no-op: everything should continue working as before. PiperOrigin-RevId: 734127195
| Commit: | 8dfe4f8 | |
|---|---|---|
| Author: | Genomics team in Google Health | |
| Committer: | Copybara-Service | |
Add methylation information to CVO PiperOrigin-RevId: 730626158
| Commit: | 15cc49c | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] Accept multi-allelic candidates * adds 2 `BaseFeatures`: `alt_indices_depth` and `alt_indices_variant_allele_frequency` * adds 2 `VariantFeatures`: `is_multiallelic` and `is_multiple_alt_alleles` features * adds field `make_examples_alt_allele_indices` to `DeepVariantCall` (the candidate proto), which instructs make_examples_native to restrict examples to the alt_allele_indices combinations that the small model did not call confidently. PiperOrigin-RevId: 726626783
| Commit: | 4e3b586 | |
|---|---|---|
| Author: | Genomics team in Google Health | |
| Committer: | Copybara-Service | |
Add option to enable methylation calling in DeepVariant PiperOrigin-RevId: 726141448
| Commit: | f32b5ef | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Move base modification parsing to nucleus. PiperOrigin-RevId: 723315638
| Commit: | d8b4083 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Part (4) of complex variants implementation. PiperOrigin-RevId: 722839178
| Commit: | 2b807f3 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
All realigning all regions. PiperOrigin-RevId: 722786313
| Commit: | 45318e2 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Add a 5mC methylation channel to deepvariant. PiperOrigin-RevId: 713528298
| Commit: | 05f0933 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Addressing the issue raised in https://github.com/google/deepvariant/issues/811 This change ensures that PL value is calculated according to the ploidy in reference blocks of gVCF. PiperOrigin-RevId: 698266848
The documentation is generated from this commit.
| Commit: | f36f747 | |
|---|---|---|
| Author: | mobinasri | |
| Committer: | Copybara-Service | |
Fixing the memory issue with GBZ reader PiperOrigin-RevId: 695498239
| Commit: | 61777eb | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add phasing info to candidate output. PiperOrigin-RevId: 683811208
| Commit: | 2b1c194 | |
|---|---|---|
| Author: | mobinasri | |
| Committer: | Copybara-Service | |
- Fixed slowness in parsing alignments from gbz. The path index is now created when the gbzReader is instantiated instead of creating an index for each query. - Instead of hard-coding context size to 1k it is now set based on the partition_size - Added a flag `--ref_chrom_prefix` for adding a prefix to the chromosome names extracted from gbz file. It is needed when we have a reference like /cns/oz-d/home/brain-genomics/pichuan/b199781544/GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.hprc_july7.fna whose chromosomes have the prefix of "GRCh38." - Renamed `pangenome_ref_name` to `ref_name_pangenome` since all other pangenome-related flags have `_pangenome` as suffix. - Removed printing runtimes in the query function of gbzReader PiperOrigin-RevId: 681641986
| Commit: | ca88780 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add an option to skip normalization in make_examples. PiperOrigin-RevId: 681532370
| Commit: | a87fd7a | |
|---|---|---|
| Author: | mobinasri | |
| Committer: | Copybara-Service | |
Added a GBZ reader to Nucleus and integrated it natively into make_examples for DeepVariant. The GBZ reader can be used to extract reads from a GBZ file. It can be slow at the moment and further optimizations will follow. PiperOrigin-RevId: 678760711
| Commit: | bfc5437 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] - Adds haplotype information to small model if `phase_reads` is enabled. - Add strand information as two features. PiperOrigin-RevId: 677840848
| Commit: | b4e1ab6 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add a sample option to skip phasing for a sample. PiperOrigin-RevId: 674437025
| Commit: | cff0882 | |
|---|---|---|
| Author: | Genomics team in Google Health | |
| Committer: | Copybara-Service | |
Automated Code Change PiperOrigin-RevId: 673655198
| Commit: | 6b74831 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | kishwarshafin | |
[small model] Enable the small model to call INDELs PiperOrigin-RevId: 663489298
| Commit: | 87f57dd | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | kishwarshafin | |
[small model] Capture additional signals (mapq, baseq, and context VAF) PiperOrigin-RevId: 657733223
| Commit: | 04f922c | |
|---|---|---|
| Author: | juancmier | |
| Committer: | kishwarshafin | |
Add functionality to blank out channels for a given variant type. PiperOrigin-RevId: 655808421
| Commit: | d2a279b | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | kishwarshafin | |
[small model] Fixes memory leak during small model inference PiperOrigin-RevId: 653710878
| Commit: | 5b3f233 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] Enable the small model to call INDELs PiperOrigin-RevId: 663489298
| Commit: | 50f4830 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] Capture additional signals (mapq, baseq, and context VAF) PiperOrigin-RevId: 657733223
| Commit: | 0fe7253 | |
|---|---|---|
| Author: | juancmier | |
| Committer: | Copybara-Service | |
Add functionality to blank out channels for a given variant type. PiperOrigin-RevId: 655808421
| Commit: | 348e2ce | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
[small model] Fixes memory leak during small model inference PiperOrigin-RevId: 653710878
| Commit: | be4cc46 | |
|---|---|---|
| Author: | juancmier | |
| Committer: | pichuan | |
This CL adds a new channel to DeepVariant that contains the average coverage of the reads aligned to any given position or base in the genome. PiperOrigin-RevId: 643492127
| Commit: | c6ec0c9 | |
|---|---|---|
| Author: | juancmier | |
| Committer: | pichuan | |
Add mean coverage estimation per sample. * Gets the total possible regions using `UNION(RefContigs, SampleContigs) - ExcludeContigs` * Uses sampling rate to get a subset of total possible regions consecutively in the middle of the possible regions. This has been tested empirically to be fast and accurate but is subject to change. * Use allele counter to process reads in each region. Allele counter already performs logic to account for cigar operations counts reads at specific positions. PiperOrigin-RevId: 645466191
| Commit: | e08da3e | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | pichuan | |
Adds `--skip_pileup_image_generation` to `make_examples` that determines if pileup images are also generated when generating small model examples. PiperOrigin-RevId: 641053022
| Commit: | 0b8f6da | |
|---|---|---|
| Author: | pichuan | |
| Committer: | pichuan | |
Add optional flags: exclude_variants_vcf_filename and exclude_variants_af_threshold. PiperOrigin-RevId: 638788722
| Commit: | 5a36126 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | pichuan | |
Add flag for downsampling training classes. PiperOrigin-RevId: 640646334
| Commit: | 76f727c | |
|---|---|---|
| Author: | shafin | |
| Committer: | pichuan | |
Internal change PiperOrigin-RevId: 636994465
| Commit: | 64d3775 | |
|---|---|---|
| Author: | koles | |
| Committer: | pichuan | |
make_example flags to support fast pipeline. PiperOrigin-RevId: 634539441
| Commit: | 42ba475 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | pichuan | |
Integrates small model variant calling with make_examples_core PiperOrigin-RevId: 625487979
| Commit: | 130b6bc | |
|---|---|---|
| Author: | pichuan | |
| Committer: | pichuan | |
Use the channels_enum_to_blank sample option in pangenome-aware implementation. PiperOrigin-RevId: 625533161
| Commit: | b0a1752 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | pichuan | |
Adds small model example generation code. PiperOrigin-RevId: 621262627
| Commit: | e154980 | |
|---|---|---|
| Author: | gjorge | |
| Committer: | pichuan | |
Small documentation fixes. PiperOrigin-RevId: 618323356
| Commit: | b693bbf | |
|---|---|---|
| Author: | danielecook | |
| Committer: | pichuan | |
Update DeepSomatic options proto. PiperOrigin-RevId: 613625838
| Commit: | d437bc8 | |
|---|---|---|
| Author: | koles | |
| Committer: | pichuan | |
Add --trim_reads_for_pileup flag. PiperOrigin-RevId: 610442006
| Commit: | 09193d8 | |
|---|---|---|
| Author: | mobinasri | |
| Committer: | pichuan | |
Pangenome aware calling PiperOrigin-RevId: 612593727
| Commit: | 0eba6d0 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | pichuan | |
In call_variants, if --include_debug_info is true, we'll incorporate the functionality in `vis.curate_pileup` to add extra annotations to the images. PiperOrigin-RevId: 603201809
| Commit: | 3fc2539 | |
|---|---|---|
| Author: | msamman | |
| Committer: | pichuan | |
remove base channels from pileup_image_native.cc PiperOrigin-RevId: 603467957
| Commit: | 83b69fe | |
|---|---|---|
| Author: | juancmier | |
| Committer: | Copybara-Service | |
Add mean coverage estimation per sample. * Gets the total possible regions using `UNION(RefContigs, SampleContigs) - ExcludeContigs` * Uses sampling rate to get a subset of total possible regions consecutively in the middle of the possible regions. This has been tested empirically to be fast and accurate but is subject to change. * Use allele counter to process reads in each region. Allele counter already performs logic to account for cigar operations counts reads at specific positions. PiperOrigin-RevId: 645466191
| Commit: | 8a36d86 | |
|---|---|---|
| Author: | juancmier | |
| Committer: | Copybara-Service | |
This CL adds a new channel to DeepVariant that contains the average coverage of the reads aligned to any given position or base in the genome. PiperOrigin-RevId: 643492127
| Commit: | 68e429e | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
Adds `--skip_pileup_image_generation` to `make_examples` that determines if pileup images are also generated when generating small model examples. PiperOrigin-RevId: 641053022
| Commit: | 48e95c6 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Add flag for downsampling training classes. PiperOrigin-RevId: 640646334
| Commit: | d96c5a8 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Add optional flags: exclude_variants_vcf_filename and exclude_variants_af_threshold. PiperOrigin-RevId: 638788722
| Commit: | 2c68cfe | |
|---|---|---|
| Author: | shafin | |
| Committer: | Copybara-Service | |
Internal change PiperOrigin-RevId: 636994465
| Commit: | 40a8cba | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
make_example flags to support fast pipeline. PiperOrigin-RevId: 634539441
| Commit: | 87ad5fc | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Use the channels_enum_to_blank sample option in pangenome-aware implementation. PiperOrigin-RevId: 625533161
| Commit: | aacaec8 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
Integrates small model variant calling with make_examples_core PiperOrigin-RevId: 625487979
| Commit: | 6991c56 | |
|---|---|---|
| Author: | lucasbrambrink | |
| Committer: | Copybara-Service | |
Adds small model example generation code. PiperOrigin-RevId: 621262627
| Commit: | f91cc35 | |
|---|---|---|
| Author: | gjorge | |
| Committer: | Copybara-Service | |
Small documentation fixes. PiperOrigin-RevId: 618323356
| Commit: | 03df409 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | kishwarshafin | |
Resolve a trivial conflict in deepvariant.proto
| Commit: | e56cfa2 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Update DeepSomatic options proto. PiperOrigin-RevId: 613625838
| Commit: | 7f0f6ff | |
|---|---|---|
| Author: | mobinasri | |
| Committer: | Copybara-Service | |
Pangenome aware calling PiperOrigin-RevId: 612593727
| Commit: | 7a9df63 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add --trim_reads_for_pileup flag. PiperOrigin-RevId: 610442006
| Commit: | d8611fd | |
|---|---|---|
| Author: | msamman | |
| Committer: | Copybara-Service | |
remove base channels from pileup_image_native.cc PiperOrigin-RevId: 603467957
| Commit: | cc11840 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
In call_variants, if --include_debug_info is true, we'll incorporate the functionality in `vis.curate_pileup` to add extra annotations to the images. PiperOrigin-RevId: 603201809
| Commit: | 1a97858 | |
|---|---|---|
| Author: | yuchenzz | |
| Committer: | Pi-Chuan Chang | |
Add a new field in DebugInfo, so we can later add activation layers outputs. PiperOrigin-RevId: 600887239
| Commit: | 0afce8c | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Pi-Chuan Chang | |
Optionally set `deterministic` for SerializedToString, which can help the testdata creation more deterministic. Add a flag to set this value, but default is False (no-op). PiperOrigin-RevId: 579340935
| Commit: | 8e0dc61 | |
|---|---|---|
| Author: | yuchenzz | |
| Committer: | Copybara-Service | |
Add a new field in DebugInfo, so we can later add activation layers outputs. PiperOrigin-RevId: 600887239
| Commit: | dbd39b5 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Optionally set `deterministic` for SerializedToString, which can help the testdata creation more deterministic. Add a flag to set this value, but default is False (no-op). PiperOrigin-RevId: 579340935
| Commit: | 28c2a0a | |
|---|---|---|
| Author: | akiraly | |
| Committer: | kishwarshafin | |
Add encoded_image in DebugInfo. PiperOrigin-RevId: 571982144
| Commit: | a25a3d1 | |
|---|---|---|
| Author: | akiraly | |
| Committer: | Copybara-Service | |
Add encoded_image in DebugInfo. PiperOrigin-RevId: 571982144
| Commit: | 493b9d5 | |
|---|---|---|
| Author: | shafin | |
| Committer: | Pi-Chuan Chang | |
Add `de_novo` label in deepvariant examples for training with `sample_weight`. PiperOrigin-RevId: 544565682
| Commit: | ae6b749 | |
|---|---|---|
| Author: | shafin | |
| Committer: | Copybara-Service | |
Add `de_novo` label in deepvariant examples for training with `sample_weight`. PiperOrigin-RevId: 544565682
| Commit: | 30cac7f | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Pi-Chuan Chang | |
Add a `--output_sitelist` flag to DeepVariant. PiperOrigin-RevId: 528879605
| Commit: | 2eff181 | |
|---|---|---|
| Author: | koles | |
| Committer: | Pi-Chuan Chang | |
Exclude non-DNA regions larger than 300,000 bases. PiperOrigin-RevId: 520783371
| Commit: | 4a35682 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Pi-Chuan Chang | |
[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. PiperOrigin-RevId: 520666963
| Commit: | 7f574af | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Pi-Chuan Chang | |
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. And, if only one sample is generating output, the code will skip adding the _sample suffix completely. PiperOrigin-RevId: 524380775
| Commit: | 82a5837 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Pi-Chuan Chang | |
Limit reads per region depending on dynamic number of bases covered. PiperOrigin-RevId: 527439333
| Commit: | 4e0d0a0 | |
|---|---|---|
| Author: | koles | |
| Committer: | Pi-Chuan Chang | |
Add optional phasing info output. PiperOrigin-RevId: 520372805
| Commit: | 49d3eb2 | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Add a `--output_sitelist` flag to DeepVariant. PiperOrigin-RevId: 528879605
| Commit: | 11e4fb6 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Limit reads per region depending on dynamic number of bases covered. PiperOrigin-RevId: 527439333
| Commit: | e39891b | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
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. And, if only one sample is generating output, the code will skip adding the _sample suffix completely. PiperOrigin-RevId: 524380775
| Commit: | ed415a5 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Exclude non-DNA regions larger than 300,000 bases. PiperOrigin-RevId: 520783371
| Commit: | b52cd1c | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
[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. PiperOrigin-RevId: 520666963
| Commit: | f163e64 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Add optional phasing info output. PiperOrigin-RevId: 520372805
| Commit: | 1c7b84a | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Internal change. PiperOrigin-RevId: 508414273
| Commit: | 4d0eb0d | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Internal change. PiperOrigin-RevId: 508184474
| Commit: | 20316b0 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Internal change. PiperOrigin-RevId: 508127777
| Commit: | e03fd88 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Internal change. PiperOrigin-RevId: 504968788
| Commit: | dcbc452 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Internal change. PiperOrigin-RevId: 504412600
| Commit: | b7a042f | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
For adding the normalize_reads field to the config used for internal scripts. PiperOrigin-RevId: 503846990
| Commit: | 538e8cb | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Set region padding for phasing according to the region length. PiperOrigin-RevId: 503528336
| Commit: | aa27de1 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
This commit is to set up a new feature contributed by Doron Shem-Tov (@doron-st) from Ultima Genomics) - for multi-sample use case, optionally enable realignment jointly among all samples. Current default behavior is that we realign each sample individually. PiperOrigin-RevId: 494850034
| Commit: | b1f1b08 | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Added option to run make_examples to generate candidate positions only. PiperOrigin-RevId: 489575282
| Commit: | 66766e3 | |
|---|---|---|
| Author: | slzarate | |
| Committer: | Copybara-Service | |
Fix typo in channel specification. PiperOrigin-RevId: 475619583
| Commit: | a60bd4d | |
|---|---|---|
| Author: | danielecook | |
| Committer: | Copybara-Service | |
Internal Update PiperOrigin-RevId: 473070351
| Commit: | 1ba2f50 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Add phase_max_candidates: If the number of candidates exceeds this number in a window, skip direct phasing. PiperOrigin-RevId: 449537411
| Commit: | ffd1516 | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Automated g4 rollback of changelist 404595398 PiperOrigin-RevId: 446832797
| Commit: | 3c5bcef | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Make DeepVariantChannelEnum. Add the corresponding code so that make_examples code will store the list of channel enum in each examples. Also, change the training code so that it generates a model.ckpt.input_info file based on the first example it sees. PiperOrigin-RevId: 441069906
| Commit: | 1e331ca | |
|---|---|---|
| Author: | pichuan | |
| Committer: | Copybara-Service | |
Update for DeepTrio Direct Phasing. PiperOrigin-RevId: 440477898
| Commit: | 307f99f | |
|---|---|---|
| Author: | koles | |
| Committer: | Copybara-Service | |
Added "reverse_haplotypes" flag to improve training using direct phasing. PiperOrigin-RevId: 437321625