Code

Create tools for SV VCF cleaning#8996

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kjaisingh wants to merge 55 commits intomasterbroadinstitute/gatk:masterfrom kj_sv_cleanvcfbroadinstitute/gatk:kj_sv_cleanvcfCopy head branch name to clipboard

+3,024

Commits

Commits on Oct 9, 2024

• Initial commit

  kjaisingh

  committed
  d8fb88c

Commits on Oct 11, 2024

• Silenced SV type processing

  kjaisingh

  committed
  0c72bd2

Commits on Oct 16, 2024

• Created initial commit for 1b

  kjaisingh

  committed
  05501ce

• Reformatting per GATK style guide

  kjaisingh

  committed
  40295e1

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

  Show description for 5cd8ea3
  

  kjaisingh

  and

  mwalker174

  authored
  5cd8ea3

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

  Show description for 75f476b
  

  kjaisingh

  and

  mwalker174

  authored
  75f476b

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

  Show description for 8d31a61
  

  kjaisingh

  and

  mwalker174

  authored
  8d31a61

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

  Show description for 12cc930
  

  kjaisingh

  and

  mwalker174

  authored
  12cc930

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

  Show description for 4ecd525
  

  kjaisingh

  and

  mwalker174

  authored
  4ecd525

Commits on Oct 17, 2024

• PR feedback

  kjaisingh

  committed
  df375cc

• Merge branch 'master' into kj_sv_cleanvcf

  kjaisingh

  committed
  6f34672

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

  kjaisingh

  committed
  2e28e13

Commits on Oct 18, 2024

• Updated to no longer ingest BED file

  kjaisingh

  committed
  f0c0e0f

• Cleaned up scripts...

  kjaisingh

  committed
  50c4eaf

• SVCleanPt2 WIP

  kjaisingh

  committed
  74de1b0

• Merge branch 'master' into kj_sv_cleanvcf

  kjaisingh

  committed
  354857f

Commits on Oct 22, 2024

• Working version of SVCleanPt2

  kjaisingh

  committed
  74f0d73

• Code cleanup

  kjaisingh

  committed
  54f5f96

• Added sorting and better formatting of outputs

  kjaisingh

  committed
  18da350

Commits on Oct 23, 2024

• Initial commit for CleanPt4

  kjaisingh

  committed
  f7e14c6

Commits on Oct 24, 2024

• WIP

  kjaisingh

  committed
  5f5a6cd

Commits on Oct 25, 2024

• WIP - up till CleanVcf5 (first task complete)

  kjaisingh

  committed
  52a9049

Commits on Oct 26, 2024

• Reformatting & restructuring

  kjaisingh

  committed
  31f7032

Commits on Oct 28, 2024

• Completed CleanVcf4 / implemented skeleton walker for CleanVcf5

  kjaisingh

  committed
  2b97b7b

Commits on Oct 30, 2024

• Revert SVCleanPt2 to use overlap buffer

  kjaisingh

  committed
  45443f9

• Working implementation of SVCleanPt5

  kjaisingh

  committed
  7fbc3a2

Commits on Oct 31, 2024

• Modified param name for chrX/chrY

  kjaisingh

  committed
  181b352

• Changes to test

  kjaisingh

  committed
  3eb5c3d

• Changes to test

  kjaisingh

  committed
  52daa21

• CleanVcf4 added exit if not in range

  kjaisingh

  committed
  d438bb9

• Updated type of EV format field

  kjaisingh

  committed
  9aaf2f1

• Minor changes - replaced EV type

  kjaisingh

  committed
  1de3e2f

Commits on Nov 1, 2024

• Merge branch 'master' into kj_sv_cleanvcf

  kjaisingh

  committed
  4e353a0

• Skip no-call genotypes

  kjaisingh

  committed
  a57601f

Commits on Nov 4, 2024

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

  kjaisingh

  committed
  2f17eec

Commits on Nov 5, 2024

• Undo use of getEnd()

  kjaisingh

  committed
  4c60608

• Furhter debugging: modified SVTYPE update & corresponding genotype assignment

  kjaisingh

  committed
  56ecaeb

• Handled no-call rewriting bug

  kjaisingh

  committed
  82ecea8

Commits on Nov 6, 2024

• Modifications to large del/dup event logic

  kjaisingh

  committed
  d96d810

• Modified conditions for biallelic filtering

  kjaisingh

  committed
  0fa7738

• Modified filter to only use distinct pairs

  kjaisingh

  committed
  a281d65

Commits on Nov 7, 2024

• Moved svtype modification to cleanpt4

  kjaisingh

  committed
  f7215ee

• Reverted svtype changes

  kjaisingh

  committed
  383a01c

Commits on Nov 12, 2024

• Merge branch 'master' into kj_sv_cleanvcf

  kjaisingh

  committed
  c9d1020

• Overlap logic change to align with GATK-SV outputs

  kjaisingh

  committed
  ee16037

• Modified overlap logic to only be unidirectional

  kjaisingh

  committed
  3f901f4

• Standardized variant overlap code

  kjaisingh

  committed
  e8ce4c5

• Modified overlap logic - minor bug

  kjaisingh

  committed
  29dc96f

Commits on Nov 14, 2024

• Modified CleanPt4 imports

  kjaisingh

  committed
  a68dcc6

Commits on Nov 18, 2024

• Minor change to remove redundant size/svtype check

  kjaisingh

  committed
  8ba660e

Commits on Nov 22, 2024

• Merge branch 'master' into kj_sv_cleanvcf

  kjaisingh

  committed
  657e601

Commits on Nov 25, 2024

• Minor file creation

  kjaisingh

  committed
  707ada6

Commits on Dec 11, 2024

• New tools - modular implementations

  kjaisingh

  committed
  1e30b4b

• Updated to include necessary imports only

  kjaisingh

  committed
  726144d

Commits on Dec 13, 2024

• Updated header writing

  kjaisingh

  committed
  0ab56eb