v5.1.2

What's Changed

• feat: Bind flag pipe through to apptainer by @SietsmaRJ in #172
• Remove Gnomad_HN and drop GRCh37 from the docs by @bartcharbon in #176
• Fix travis PyPi deploy by @bartcharbon in #178

Full Changelog: v5.1.1...v5.1.2

v5.1.1

What's Changed

• Fix for multithreading not adhering to set value (also increases train speed). by @svandenhoek in #167
• Fixed a bug that would force the predict output file to always be gzipped (explain) by @svandenhoek in #168
• fix: Output overwrite without force by @SietsmaRJ in #165
• Fix/removed legacy code + general code improvements by @svandenhoek in #170
  • includes xgboost updated to 1.7.4
• version bump by @svandenhoek in #171

Full Changelog: v5.1.0...v5.1.1

v5.1.1 models: Improved CAPICE models trained on CAPICE version 5.1.1 including the GnomAD Homozygosity counts feature. Validation can be found here.

v5.1.0

What's Changed

• Updated xgboost to 1.7.3 by @svandenhoek in #157
• Feat/easybuild to apptainer + README/setupy.py adjustments by @SietsmaRJ in #156
• chore: Re-add gnomAD_HN feature by @SietsmaRJ in #162
• docs: Conversion script pointer by @SietsmaRJ in #160
• fix: Rollback to 4.0.0 output column names by @SietsmaRJ in #159
• chore: Update and equalize dependencies by @SietsmaRJ in #163
• chore: CAPICE 5.1.0 version bump by @SietsmaRJ in #161

Full Changelog: v5.0.0...v5.1.0

v5.0.0

What's Changed

• README updates: Added info about Singularity image and added section with original sources data by @svandenhoek in #142
• feat: Improved intron-exon splitting by @SietsmaRJ in #143
• Revert "feat: Improved intron-exon splitting" by @svandenhoek in #145
• feat: Move balancing script by @SietsmaRJ in #146
• Feat/xgboost version bump by @svandenhoek in #144
• fix/input digestion (error), minimal required python version & travis by @svandenhoek in #147
• Feat/json models by @svandenhoek in #151
• Fixed a bug that would force the predict output file to always be gzipped by @svandenhoek in #154
• Fix/train feature json by @SietsmaRJ in #153

Full Changelog: v4.0.0...v5.0.0

For the models:
v1: Initial release of CAPICE 5.0.0.
v2: Updated model (trained at tag 5.1.0) including the GnomAD homozygous counts for improved performance.

v4.0.0

What's Changed

• feat: No Imputing by @SietsmaRJ in #130
• feat: Updated libraries by @SietsmaRJ in #131
• Feat/simplified bcftools by @SietsmaRJ in #135
• Uniform extra_require naming between repo's. by @svandenhoek in #136
• Feat/new features + VEP update by @svandenhoek in #137
• chore: Primary branch rename by @SietsmaRJ in #140
• feat: Informative train info log by @SietsmaRJ in #138
• feat: 4.0.0 Release by @SietsmaRJ in #141

Full Changelog: v3.3.0...v4.0.0

For the models:
v1: Initial release of CAPICE 4.0.0.
v2: Updated model with improved training process (no heterozygous variants in autosomal recessive genes)

v4.0.0-rc3

What's Changed

• Feat/simplified bcftools by @SietsmaRJ in #135
• Uniform extra_require naming between repo's. by @svandenhoek in #136
• Feat/new features + VEP update by @svandenhoek in #137

Full Changelog: v4.0.0-rc2...v4.0.0-rc3

v4.0.0-rc2

What's Changed

• feat: Updated libraries by @SietsmaRJ in #131

Full Changelog: v4.0.0-rc1...v4.0.0-rc2

v4.0.0-rc1

What's Changed

• feat: No Imputing by @SietsmaRJ in #130

Full Changelog: v3.3.0...v4.0.0-rc1

v3.3.0

What's Changed

• fix: Allele frequency support by @SietsmaRJ in #133

Full Changelog: v3.2.1...v3.3.0

v3.2.1

What's Changed

• fix: raw train file by @SietsmaRJ in #122
• fix: Index in train TSV by @SietsmaRJ in #124
• fix: README VEP duplicate flag by @SietsmaRJ in #129
• fix: Train input raw by @SietsmaRJ in #132

Full Changelog: v3.2.0...v3.2.1