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Create tools for SV VCF cleaning#8996

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kjaisingh wants to merge 61 commits intomasterbroadinstitute/gatk:masterfrom kj_sv_cleanvcfbroadinstitute/gatk:kj_sv_cleanvcfCopy head branch name to clipboard

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Commits on Oct 9, 2024

• Initial commit

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  d8fb88c

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Commits on Oct 11, 2024

• Silenced SV type processing

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Commits on Oct 16, 2024

• Created initial commit for 1b

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• Reformatting per GATK style guide

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  40295e1

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• Update src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVCleanPt1a.java

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• Update src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVCleanPt1a.java

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• Update src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVCleanPt1a.java

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• Update src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVCleanPt1a.java

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• Update src/main/java/org/broadinstitute/hellbender/tools/walkers/sv/SVCleanPt1a.java

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Commits on Oct 17, 2024

• PR feedback

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• Merge branch 'master' into kj_sv_cleanvcf

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• WIP commit - prior to deprecating BED file input in 1b

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Commits on Oct 18, 2024

• Updated to no longer ingest BED file

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  f0c0e0f

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• Cleaned up scripts...

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• SVCleanPt2 WIP

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• Merge branch 'master' into kj_sv_cleanvcf

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Commits on Oct 22, 2024

• Working version of SVCleanPt2

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• Code cleanup

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• Added sorting and better formatting of outputs

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Commits on Oct 23, 2024

• Initial commit for CleanPt4

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Commits on Oct 24, 2024

• WIP

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Commits on Oct 25, 2024

• WIP - up till CleanVcf5 (first task complete)

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Commits on Oct 26, 2024

• Reformatting & restructuring

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Commits on Oct 28, 2024

• Completed CleanVcf4 / implemented skeleton walker for CleanVcf5

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  2b97b7b

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Commits on Oct 30, 2024

• Revert SVCleanPt2 to use overlap buffer

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• Working implementation of SVCleanPt5

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  7fbc3a2

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Commits on Oct 31, 2024

• Modified param name for chrX/chrY

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• Changes to test

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• Changes to test

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  52daa21

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• CleanVcf4 added exit if not in range

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  d438bb9

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• Updated type of EV format field

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  9aaf2f1

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• Minor changes - replaced EV type

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Commits on Nov 1, 2024

• Merge branch 'master' into kj_sv_cleanvcf

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• Skip no-call genotypes

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Commits on Nov 4, 2024

• Changes post-debugging: modify .getEnd() to use SVLEN

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Commits on Nov 5, 2024

• Undo use of getEnd()

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• Furhter debugging: modified SVTYPE update & corresponding genotype assignment

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• Handled no-call rewriting bug

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Commits on Nov 6, 2024

• Modifications to large del/dup event logic

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  d96d810

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• Modified conditions for biallelic filtering

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• Modified filter to only use distinct pairs

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Commits on Nov 7, 2024

• Moved svtype modification to cleanpt4

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• Reverted svtype changes

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Commits on Nov 12, 2024

• Merge branch 'master' into kj_sv_cleanvcf

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• Overlap logic change to align with GATK-SV outputs

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  ee16037

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• Modified overlap logic to only be unidirectional

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  3f901f4

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• Standardized variant overlap code

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  e8ce4c5

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• Modified overlap logic - minor bug

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  29dc96f

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Commits on Nov 14, 2024

• Modified CleanPt4 imports

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Commits on Nov 18, 2024

• Minor change to remove redundant size/svtype check

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Commits on Nov 22, 2024

• Merge branch 'master' into kj_sv_cleanvcf

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Commits on Nov 25, 2024

• Minor file creation

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Commits on Dec 11, 2024

• New tools - modular implementations

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  1e30b4b

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• Updated to include necessary imports only

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Commits on Dec 13, 2024

• Updated header writing

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Commits on Jan 13, 2025

• Added sex revisions for male GT

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Commits on Jan 17, 2025

• Concatenated overlapping cnv tasks into one

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• Merge branch 'master' into kj_sv_cleanvcf

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Commits on Jan 21, 2025

• Bug-fixed to match results from 5-pass version

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• Standardized overlap logic across OverlappingCnv task methods

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Commits on Jan 29, 2025

• Used caching to improve runtime

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