Code

PCR primer filter#4499

Code

Merged

adamnovak merged 51 commits intomastervgteam/vg:masterfrom primer-filtervgteam/vg:primer-filterCopy head branch name to clipboardJan 23, 2025

+2,177-1

Commits

Commits on Oct 6, 2023

• point submods at same commit of libhandlegraph

  jeizenga

  committed
  4e5ef9e

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• update libvgio

  jeizenga

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  99c3954

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• resolve merge conflicts

  AlanZhangUCSC

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Commits on Oct 11, 2023

• save

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  2d4be84

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• update

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Commits on Oct 13, 2023

• update

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Commits on Oct 16, 2023

• update

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  02dac08

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• update something

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  57016df

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• more optimized

  AlanZhangUCSC

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• added comments

  AlanZhangUCSC

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  6a2f0bf

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Commits on Oct 17, 2023

• unittest

  AlanZhangUCSC

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• start on interface

  AlanZhangUCSC

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• update

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• update

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• Merge pull request #2 from AlanZhangUCSC/primers

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Commits on Oct 18, 2023

• multiple reference paths

  AlanZhangUCSC

  committed
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• beautify

  AlanZhangUCSC

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Commits on Oct 19, 2023

• update

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Commits on Oct 20, 2023

• Merge pull request #3 from AlanZhangUCSC/primers_by_chrom

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• update

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• Merge pull request #4 from AlanZhangUCSC/primers_by_chrom

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• rm

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Commits on Oct 23, 2023

• up

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• integration test

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Commits on Oct 24, 2023

• up

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• up

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Commits on Oct 28, 2023

• update

  

  Alan Zhang

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Commits on Oct 30, 2023

• fix bug

  AlanZhangUCSC

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  9c364fe

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Commits on Nov 14, 2023

• up

  AlanZhangUCSC

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  a49b43a

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• Merge pull request #5 from AlanZhangUCSC/with_reference_coordinates

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Commits on Dec 30, 2024

• Merge AlanZhangUCSC/vg except for deps/xg and deps/libbdsg

  xchang1

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• Fix typos

  xchang1

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  d7b6fc9

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• Add wiki page for primer filtering but in the wrong directory

  xchang1

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Commits on Jan 3, 2025

• Make primer finder use the unformatted primer3 output

  xchang1

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  6f37a84

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• Map template sequence if the given path isn't in the graph

  xchang1

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Commits on Jan 6, 2025

• Check more ways of being wrong

  xchang1

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• Check that the graph has the path surject used

  xchang1

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  c4e9e68

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• Use zipcodes and long read code path (kind of) but I havne't merged the real long read branch yet

  xchang1

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• Merge remote-tracking branch 'upstream/lr-giraffe' into primer-filter

  xchang1

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• Use zipcodes in primer unit test

  xchang1

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Commits on Jan 9, 2025

• add mor checks for bad alignments

  xchang1

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Commits on Jan 19, 2025

• Merge remote-tracking branch 'upstream/master' into primer-filter

  xchang1

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  db8d6f8

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• Rename snarl index as distance index to avoid confusion

  xchang1

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  e811a4c

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• Make minimizer index accessible to giraffe

  xchang1

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  645f5c7

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• Make sure the minimizer mapper sticks around

  xchang1

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  9f8cb5f

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Commits on Jan 20, 2025

• Move wiki page to wiki

  xchang1

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  ec78bdf

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• Update wiki

  xchang1

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  b6493ef

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• Fix integration test for vg primers

  xchang1

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  1e911f9

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• Fix primer test files

  xchang1

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  4b8f33f

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• Fix format of test file

  xchang1

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  a57c351

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• Change unit test file names to assume it is being run from the test directory

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