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Commits on Oct 19, 2023

• Implementation of MergeReads method and unit tests.

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Commits on Oct 3, 2023

• Python API added to report variant phasing.

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Commits on Sep 25, 2023

• Special post processing for Somatic variants.

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• Special somatic post processing added.

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Commits on Sep 21, 2023

• Fix for the direct_phasing reset.

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Commits on Sep 14, 2023

• CompareGroups method added to Merger class.

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Commits on Sep 13, 2023

• Automated g4 rollback of changelist 564452574

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• Do not allow duplicate reads in allele support.

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Commits on Sep 11, 2023

• Split VCF output in somatic mode. New flag allows to output somatic variants into a separate VCF. The flag is not compatible with GVCF.

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Commits on Aug 29, 2023

• Get abseil-cpp from GitHub repo and pin it to the latest version.

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Commits on Aug 3, 2023

• GroupReads, UpdateReadsMap methods added.

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Commits on Jul 14, 2023

• MergePhasedReads script: LoadFiles function is added.

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Commits on Jun 25, 2023

• Function to parse sharded file spec is added.

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Commits on Jun 14, 2023

• Fix the edge case in align_to_all_haplotypes.

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Commits on Jun 9, 2023

• Setup merge_phased_reads cc binary.

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Commits on Jun 2, 2023

• Header file for merge_phased_reads implementation.

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Commits on Apr 21, 2023

• Implement get_candidate_positions for VcfImporter to allow direct phasing with imported candidates.

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Commits on Apr 13, 2023

• Automated g4 rollback of changelist 524070859

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Commits on Apr 11, 2023

• Pass allele_counters by pointer to improve a runtime performance.

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Commits on Mar 31, 2023

• Improve find_ref_n_regions algorithm.

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• Exclude non-DNA regions larger than 300,000 bases.

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Commits on Mar 29, 2023

• Add optional phasing info output.

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Commits on Mar 25, 2023

• Special processing for non_autosomes chromosomes.

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Commits on Mar 7, 2023

• Add missing include <string>

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• Automated g4 rollback of changelist 514019312

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Commits on Mar 6, 2023

• Automated g4 rollback of changelist 514027408

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Commits on Feb 27, 2023

• Small edit in ONT duplex case study.

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• Small correction in case study.

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Commits on Feb 17, 2023

• Set default value for USE_CANDIDATE_PARTITION variable.

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Commits on Feb 8, 2023

• Internal change.

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Commits on Feb 7, 2023

• Internal change.

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Commits on Jan 24, 2023

• Add candidate partitioning functionality to run_deepvariant and run_deeptrio docker scripts.

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Commits on Jan 23, 2023

• Internal change.

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Commits on Jan 20, 2023

• Set region padding for phasing according to the region length.

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Commits on Jan 9, 2023

• Optimize memory usage when reading input BAM files.

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