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Commits on Oct 26, 2022

• Update HIVDB to 9.2; need update conditionalComments too

  philiptzou

  committed
  0c0aab2

Commits on Oct 19, 2022

• Upgrade to Java 15

  philiptzou

  committed
  6b5c41a

Commits on Oct 18, 2022

• Update algorithms/versions.json

  philiptzou

  committed
  d36e5b0

• Add ANRS 31/32/33

  philiptzou

  committed
  e1af98c

Commits on Oct 12, 2022

• Anchor two AAs insertion to IN:255

  philiptzou

  committed
  d811713

• Add notes for removed leading/trailing Ns

  philiptzou

  committed
  e536fc4

Commits on Oct 6, 2022

• Avoid using MutationSet::filterBy if filterByNoSplit can also be used

  philiptzou

  committed
  61e91f7

• Tweak minimap2 alignment opts and add support for using conditionally unsequenced regions

  Show description for d56c9f8
  philiptzou

  committed
  d56c9f8

Commits on Aug 30, 2022

• Add patterns_hiv1.json

  philiptzou

  committed
  cc76791

• Add patterns_hiv1

  philiptzou

  committed
  cc952ee

Commits on Jul 21, 2022

• Should also update alignment-config_hiv1.json

  philiptzou

  committed
  d3ecec4

• Increase the tolerance of HIV-1 alignment to allow aligning short sequence

  philiptzou

  committed
  8116af9

Commits on Jul 17, 2022

• Remove the "click Read Coverage" button warning

  philiptzou

  committed
  f711b57

Commits on Jul 13, 2022

• Set HIV-1's defaultIncludedGenes to [PR, RT, IN]

  philiptzou

  committed
  fbf4776

Commits on Jul 8, 2022

• Change validation level for DRP so it doesn't trigger CRITICAL error

  philiptzou

  committed
  1e69442

Commits on Jul 7, 2022

• build and test should also depends on copyData

  philiptzou

  committed
  10c1358

Commits on Jul 5, 2022

• Add refRanges to gene defs

  philiptzou

  committed
  1edb805

Commits on Jul 4, 2022

• Update HIV2 data

  philiptzou

  committed
  1d5dfd7

Commits on Jul 1, 2022

• When getGenes() or getDrugClasses(), the results from map should be distincted

  philiptzou

  committed
  1ac356b

Commits on Jun 29, 2022

• Update HIV and HIV2 interface

  philiptzou

  committed
  dbaea65

Commits on Jun 16, 2022

• Improve DR position validation messages

  philiptzou

  committed
  4910ba2

• Update assembly-config of hiv1 to use CA, PR, RT, and IN for assembling

  philiptzou

  committed
  f839500

• Clean up HIV-1 validation messages

  philiptzou

  committed
  1eb96f4

• Add back PR/RT/IN DRMs to usual and add CA DRMs to usual

  philiptzou

  committed
  8d75502

• Fix field types

  philiptzou

  committed
  276ec39

• Update Capsid data

  philiptzou

  committed
  391f051

• Add includeGenes to mutation validators

  philiptzou

  committed
  f76c016

• Tweak alignment parameters

  philiptzou

  committed
  0460668

• Add support for includeGenes and fix sequence assembler config

  philiptzou

  committed
  9aa7463

• Fix alignment-config and genes

  philiptzou

  committed
  a78bd26

• Fix alignment-config

  philiptzou

  committed
  9b8d370

• Bump Gradle to 7.3.2

  philiptzou

  committed
  062fab2

• Update alignment-config for HIV-1 to cover whole genome

  philiptzou

  committed
  9dda878

• Fix assembly-config_hiv1

  philiptzou

  committed
  c6a09f1

• Fix postProcessors command

  philiptzou

  committed
  06271e8

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