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Autoindex zipcodes#4455

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xchang1 wants to merge 17 commits intovgteam:lr-giraffevgteam/vg:lr-giraffefrom xchang1:autoindex-zipcodesxchang1/vg:autoindex-zipcodesCopy head branch name to clipboard

+261-81

Commits

Commits on Oct 22, 2024

• Add option to sort by alignment score but break ties with chain scores

  xchang1

  committed
  4bb81db

• Fix bug

  xchang1

  committed
  bb1f31d

Commits on Oct 23, 2024

• Fix order

  xchang1

  committed
  875f432

Commits on Nov 22, 2024

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

  xchang1

  committed
  c5194dc

• Take out old scoring by chain score because it didn't help

  xchang1

  committed
  0c40b14

• Serialize the zipcodes with the minimizers in autoindex

  xchang1

  committed
  abf3e4a

Commits on Nov 25, 2024

• Add lr-giraffe option to autoindex with minimizer parameters

  xchang1

  committed
  ffaab17

• Make giraffe subcommand use the index registry's zipcodes

  xchang1

  committed
  626f925

• Fix zipcode file in output of recipe

  xchang1

  committed
  ae25abf

• Make giraffe build long read minimizers for long read presets

  xchang1

  committed
  1c97950

Commits on Nov 26, 2024

• Make minimizer weighting parameters part of the autoindex parameters

  xchang1

  committed
  f3792b8

• Split up short and long read minimizer making

  xchang1

  committed
  03ed290

• Actually use long read parameters

  xchang1

  committed
  b453f4c

• Make giraffe pick which indexes to use

  xchang1

  committed
  3f37c9a

• Add an autoindex option to start from a gbz file

  xchang1

  committed
  be42c30

• Make autoindexer guess at and use files that weren't provided

  xchang1

  committed
  76c6f2c

• Take out unnecesary string constructor

  xchang1

  committed
  b8048df