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CHANGELOG.md

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Changelog

1.11.7 (2024-09-12)

Bug Fixes

  • Only append labels in first iteration of storage loop; calculate chi2 only on non empty feature matrix. (#96) (20a469a)
  • restrict calls to reference contigs (#101) (0413580)

1.11.6 (2024-08-06)

Bug Fixes

  • hide sort_index in results table (#94) (bb72674)

1.11.5 (2024-07-12)

Performance Improvements

  • update to latest datvzrd (2ae57cc)

1.11.4 (2024-07-08)

Bug Fixes

  • update to latest datavzrd wrappers (ba6b039)

1.11.3 (2024-06-28)

Bug Fixes

  • fix f* calculation (#89) (1afb621)
  • Split intersection with target region and normalize calls in separate rules. (#90) (795a82b)

1.11.2 (2024-06-24)

Performance Improvements

  • update to latest datavzrd (includes sorting and column hiding) (#87) (182edbb)

1.11.1 (2024-06-23)

Bug Fixes

1.11.0 (2024-06-20)

Features

  • add F*-measure (#84) (92f4903)
  • add seqc2 wgs and ffpe to presets (#82) (c475b0f)
  • add version of benchmark as key in presets and include in report (#80) (111b4ec)
  • offer download of datavzrd reports as excel (#81) (6f5055e)

1.10.0 (2024-06-11)

Features

  • improve coverage stratification for datasets with high coverage (#75) (225113c)

Bug Fixes

  • change bm names to adhere to naming scheme in pm4onco (#78) (20ad65e)

1.9.0 (2024-05-17)

Features

  • expand benchmarking datasets with IMGAG somatic validation data (#61) (307e034)
  • Liftover callsets from hg19/GRCh37 to hg38/GRCh38 (#70) (28f96a8)
  • only consider PASS and no-filter variants in given callsets (#66) (7c48a8c)
  • stratification of VAFs (#68) (8d2c121)

Bug Fixes

  • fix failing giab testcase (#72) (5f24c56)
  • imgag-somatic and integrate seqc2 (#63) (274d800)
  • merge truthsets (#71) (aa8ca0a)
  • rename-contigs to include target bed intersection and add mapping files to resources (#73) (65930c5)
  • use latest datavzrd wrapper, integrating templating of config, thereby avoiding leaks of local storage paths into datavzrd config (#74) (40a64ed)

1.8.5 (2023-11-13)

Performance Improvements

1.8.4 (2023-09-28)

Bug Fixes

  • avoid issue that occurs with single callset (#57) (c41b1c3)

1.8.3 (2023-07-12)

Bug Fixes

  • work around issues with --all-temp and the checkpoint output (1c8a11f)

1.8.2 (2023-07-11)

Features

  • limit the number of entries to be shown in the FP/FN tables (7b2cc19)

Miscellaneous Chores

1.8.1 (2023-07-11)

Bug Fixes

  • omit index creation in FP/FN collection (aa090b1)

1.8.1 (2023-07-11)

Bug Fixes

  • omit index creation in FP/FN collection (aa090b1)

1.8.0 (2023-07-11)

Features

  • chunked processing of fp/fn collection in order to save memory (#51) (a36a13b)

1.7.4 (2023-07-03)

Performance Improvements

  • update to latest datavzrd (fb0127c)

1.7.3 (2023-06-21)

Bug Fixes

  • use a precision of 3 for displaying floats in datavzrd, use an FDR threshold of 0.25 in order to see more borderline cases (237b86c)

1.7.2 (2023-06-14)

Performance Improvements

1.7.1 (2023-05-30)

Bug Fixes

  • use 10% FDR threshold for correlation test (b596fa3)
  • use p-value <=0.05 for filtering chi-square results instead of FDR. While the FDR is still displayed, this better allows to check individual results without being influenced by the amount of multiple testing. (096ffd0)

1.7.0 (2023-05-25)

Features

  • add plot view of precision and recall (28e4249)

1.6.7 (2023-05-04)

Bug Fixes

  • define retries for fallible rules (#41) (2f7dddf)
  • error out if a callset does not match the truth at all (#43) (480b929)

Performance Improvements

  • update to latest datavzrd (8022a46)

1.6.6 (2023-04-27)

Bug Fixes

  • fixes for custom benchmarks and cleanup of chi2 output (#39) (c8cdfb8)

1.6.5 (2023-03-20)

Bug Fixes

  • use Benjamini/Yekutieli method for FDR correction (9391a1a)

1.6.4 (2023-02-12)

Bug Fixes

  • use resources to set sort threads (ed5bca0)

1.6.3 (2023-02-12)

Bug Fixes

1.6.2 (2023-01-13)

Bug Fixes

  • correct columns in case of empty precision recall (#33) (03e60da)
  • display of false negatives (#35) (b3feca6)

1.6.1 (2023-01-10)

Bug Fixes

Performance Improvements

1.6.0 (2023-01-10)

Features

  • replace hap.py with direct use of vcfeval (#30) (75113fa)

1.5.1 (2022-11-11)

Bug Fixes

  • add common to source files (f4c9d0b)
  • drop empty rows (#29) (87b85dc)
  • Use common module as input for the correct rules. This fixes the deployment of this workflow as a module. (7a00a2f)

1.5.0 (2022-10-27)

Features

  • improved precision recall reporting (#25) (5f5d18f)
  • improved, interactive reporting (FP/FN and precision/recall) (#27) (df6e430)

Performance Improvements

1.4.1 (2022-08-25)

Bug Fixes

  • improved genome and benchmark parsing and collection (#22) (07934ad)

1.4.0 (2022-08-25)

Features

  • collect FP and FN calls and compare them across callsets (#18) (cca4571)

Performance Improvements

  • update snakemake wrappers to v1.7.2 (#19) (65ffae3)

1.3.6 (2022-07-20)

Bug Fixes

  • fix genotype-ignoring recall computation (a83f00d)

1.3.5 (2022-06-08)

Bug Fixes

  • fix samtools sort argument when retrieving reads (05abcae)

1.3.4 (2022-05-09)

Bug Fixes

1.3.3 (2022-05-05)

Bug Fixes

1.3.2 (2022-05-05)

Bug Fixes

1.3.1 (2022-05-05)

Bug Fixes

  • use latest bwa wrapper to avoid issues with mamba pulling an old r-base package (9a53ad0)

1.3.0 (2022-05-05)

Features

Bug Fixes

  • define target bed as local input file if not a URL (#8) (a2c9844)

1.2.0 (2022-03-15)

Features

  • Generalize towards being able to use other genomes than NA12878 (#6) (741d8df)

1.1.0 (2022-02-10)

Features

  • generalization to allow multiple callsets and arbitrary benchmark datasets (#4) (52cef3a)

1.0.1 (2021-12-20)

Bug Fixes

  • allow missing variant-calls key (1c9c853)

1.0.0 (2021-12-20)

Features

  • allow to limit workflow to given regions (6e3792a)
  • allow to specify custom reads instead of downloading public data in the workflow (cee1a05)
  • plot numbers in precision-recall plot (6899ee1)
  • support multiple callsets (65268e4)

Bug Fixes

  • custom read handling (04057c1)
  • ensure that stratified regions do not contain duplicate entries (5dbafc9)
  • fixed error with uninitialized variable (1209946)
  • handling of custom reads (1bad2fc)
  • merge overlapping regions (5e4c928)
  • mosdepth output path (d6af6a3)
  • removed superfluous argument (ec259d1)
  • sort regions before merging them (9a3c8af)
  • typo (283e05f)
  • typo (68ae86b)
  • typo in rule all (894775f)