diff --git a/.bumpversion.toml b/.bumpversion.toml index 039b57af..54cd5e07 100644 --- a/.bumpversion.toml +++ b/.bumpversion.toml @@ -1,5 +1,5 @@ [tool.bumpversion] -current_version = "2.3.1.9001" +current_version = "2.3.1.9002" search = "{current_version}" replace = "{new_version}" message = "Bump version: {current_version} → {new_version}" diff --git a/.github/workflows/build_conda_recipes.yaml b/.github/workflows/build_conda_recipes.yaml index b576f803..54efdca4 100644 --- a/.github/workflows/build_conda_recipes.yaml +++ b/.github/workflows/build_conda_recipes.yaml @@ -12,7 +12,7 @@ env: conda_env_yaml: conda/env/yaml conda_env_lock: conda/env/lock conda_org: pcgr - VERSION: '2.3.1.9001' # bump + VERSION: '2.3.1.9002' # bump jobs: conda_build: # When merging to one of the branches above and the commit message matches diff --git a/conda/env/lock/pcgr-linux-64.lock b/conda/env/lock/pcgr-linux-64.lock index d8f4ade5..5c03bc10 100644 --- a/conda/env/lock/pcgr-linux-64.lock +++ b/conda/env/lock/pcgr-linux-64.lock @@ -1,45 +1,48 @@ # Generated by conda-lock. # platform: linux-64 -# input_hash: 868c4c18f3fadbaa7bd7a61f045f2b530f3721bcdad9ba4ba30c6c41ca08f354 +# input_hash: d780795cc80def57ebdf9871c5dde4a5d6cc61713d27c24f5ea50a0b2e04c64f @EXPLICIT https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-4.18.0-he073ed8_9.conda#86d9cba083cd041bfbf242a01a7a1999 https://conda.anaconda.org/conda-forge/linux-64/mpi-1.0-openmpi.tar.bz2#1dcc49e16749ff79ba2194fa5d4ca5e7 -https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.10-ha770c72_0.conda#a4b80dd6e9e0784ba48e6803bef1e17a +https://conda.anaconda.org/conda-forge/linux-64/pandoc-3.10.1-ha770c72_0.conda#2e6769cee7eb33dc5780994f816305e6 https://conda.anaconda.org/conda-forge/noarch/python_abi-3.12-8_cp312.conda#c3efd25ac4d74b1584d2f7a57195ddf1 -https://conda.anaconda.org/conda-forge/noarch/tzdata-2025c-hc9c84f9_1.conda#ad659d0a2b3e47e38d829aa8cad2d610 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https://conda.anaconda.org/conda-forge/osx-64/liblzma-5.8.3-hbb4bfdb_0.conda#becdfbfe7049fa248e52aa37a9df09e2 https://conda.anaconda.org/conda-forge/osx-64/libntlm-1.8-h6e16a3a_0.conda#23d706dbe90b54059ad86ff826677f39 -https://conda.anaconda.org/conda-forge/osx-64/libtasn1-4.21.0-hf3981d6_0.conda#3f1d3561577d92546eed3cc988cfe69b +https://conda.anaconda.org/conda-forge/osx-64/libtasn1-4.21.0-ha1e9b39_1.conda#c85e8026e879717c175a37bdbe2a0e73 https://conda.anaconda.org/conda-forge/osx-64/libzlib-1.2.13-h87427d6_6.conda#c0ef3c38a80c02ae1d86588c055184fc https://conda.anaconda.org/conda-forge/osx-64/llvm-openmp-22.1.8-h0d3cbff_0.conda#9d5828c46147a47f828ca47a18407621 https://conda.anaconda.org/conda-forge/osx-64/macports-legacy-support-1.3.0-hfdf4475_0.conda#08f41941a3154f2ed18f61e4a4cb8776 @@ -43,7 +43,7 @@ https://conda.anaconda.org/conda-forge/osx-64/perl-compress-raw-zlib-2.214-pl532 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https://conda.anaconda.org/conda-forge/osx-64/pymongo-4.17.0-py312h959a22e_0.conda#6c7456a1d949d92a2d9657b1d757f54d https://conda.anaconda.org/conda-forge/osx-64/zstandard-0.23.0-py312h2f459f6_3.conda#f53fa375c2e4a2e42a64578db302145d https://conda.anaconda.org/conda-forge/osx-64/clang-18.1.7-default_ha3b9224_0.conda#f3d140dbce64634d0c77665d9a4e7ccb https://conda.anaconda.org/conda-forge/osx-64/libcblas-3.11.0-8_h9b27e0a_openblas.conda#4f116127b172bbba835c1e0491efd86f https://conda.anaconda.org/conda-forge/osx-64/liblapack-3.11.0-8_h859234e_openblas.conda#e11ee849bd2a573a0f6e53b1b67ebf37 -https://conda.anaconda.org/bioconda/noarch/perl-libwww-perl-6.82-pl5321hdfd78af_0.conda#aa22aaf9aa96485cbf6e8ab1501bb7c4 +https://conda.anaconda.org/bioconda/noarch/perl-libwww-perl-6.83-pl5321hdfd78af_0.conda#24683a2fa15544a5bae791ed6bf0c109 https://conda.anaconda.org/conda-forge/noarch/urllib3-2.5.0-pyhd8ed1ab_0.conda#436c165519e140cb08d246a4472a9d6a https://conda.anaconda.org/conda-forge/osx-64/clangxx-18.1.7-default_ha3b9224_0.conda#a0432972cebd01c75aba04f1983e9919 https://conda.anaconda.org/conda-forge/osx-64/gsl-2.7-h93259b0_0.tar.bz2#b4942b1ee2a52fd67f446074488d774d @@ -276,15 +277,15 @@ https://conda.anaconda.org/conda-forge/noarch/requests-2.34.2-pyhcf101f3_0.conda https://conda.anaconda.org/bioconda/osx-64/bcftools-1.21-h0126a07_0.tar.bz2#5d8a98bddbd3096ad683ea1417d229ff https://conda.anaconda.org/conda-forge/noarch/compiler-rt_osx-64-18.1.7-h7312ed1_0.conda#fc8018d68760e1345dee2754738b1bf1 https://conda.anaconda.org/bioconda/osx-64/cyvcf2-0.31.1-py312hda6e3e2_1.tar.bz2#1fe8bff7f489d909d78dd65cf0d2d1ab -https://conda.anaconda.org/bioconda/osx-64/hmmer-3.4-hc70aa7a_4.tar.bz2#3dd504dd328023abe1373ce827581854 +https://conda.anaconda.org/bioconda/osx-64/hmmer-3.4-ha2f04f8_5.conda#2baf4438a236855ac685a3367c9f9904 https://conda.anaconda.org/pcgr/noarch/oncokb-annotator-3.4.1.9000-py_0.conda#4f4a8e7191568018f74eccd095a92fa5 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https://conda.anaconda.org/conda-forge/osx-64/r-sourcetools-0.1.7_2-r45h384437d_0.conda#afd1a125ebcb2387d547cc8a4c6b043e https://conda.anaconda.org/conda-forge/noarch/r-squarem-2026.1-r45hc72bb7e_0.conda#b8a3906de179464adc9e2dcf005cfeaf -https://conda.anaconda.org/conda-forge/osx-64/r-stringi-1.8.7-r45h64d3038_2.conda#d39d22e6a04cd39ab54925210ac949e1 +https://conda.anaconda.org/conda-forge/osx-64/r-stringi-1.8.9-r45h64d3038_0.conda#61f3566b1c9752aad6dcd8d8f017c695 https://conda.anaconda.org/conda-forge/osx-64/r-sys-3.4.3-r45h735ac91_1.conda#fce9523c92ae8be9e7d13b626d40b9c4 https://conda.anaconda.org/conda-forge/noarch/r-timedate-4052.112-r45hc72bb7e_0.conda#b9ce34da7db4d27de7a478d629b1b2b0 https://conda.anaconda.org/conda-forge/osx-64/r-utf8-1.2.6-r45h735ac91_1.conda#d1f457be352ee40e54cc1c99d3e27ac3 https://conda.anaconda.org/conda-forge/noarch/r-viridislite-0.4.3-r45hc72bb7e_0.conda#bcadc0a3726e2191e51449f67fa5e0a9 https://conda.anaconda.org/conda-forge/noarch/r-withr-3.0.3-r45hc72bb7e_0.conda#388d25e67f93a5fec2aebe56d6a0a1d9 -https://conda.anaconda.org/conda-forge/osx-64/r-xfun-0.59-r45h8eed41d_0.conda#1cc93c0629eb86f23fadd2e16163afea +https://conda.anaconda.org/conda-forge/osx-64/r-xfun-0.60-r45h8eed41d_0.conda#12fdcfc1e7ab4db6d88b3be1225a5986 https://conda.anaconda.org/conda-forge/osx-64/r-xml-3.99_0.23-r45h250ee6c_0.conda#65c2931d977c5363c603f43a1b4a9cc4 https://conda.anaconda.org/conda-forge/noarch/r-xtable-1.8_8-r45hc72bb7e_0.conda#e18fda0821f0fdc1c34276c5e0acdc92 https://conda.anaconda.org/conda-forge/osx-64/r-yaml-2.3.12-r45h735ac91_0.conda#bc0dcd3a525ac4c238c2098b31f33638 @@ -219,7 +218,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-diagram-1.6.5-r45ha770c72_4.cond https://conda.anaconda.org/conda-forge/osx-64/r-ellipsis-0.3.3-r45h8eed41d_0.conda#05c8908fbcc12ed07762cf05aa7738f5 https://conda.anaconda.org/conda-forge/noarch/r-foreach-1.5.2-r45hc72bb7e_4.conda#5abe392c8f8c5b954ebdc5fe46fcc709 https://conda.anaconda.org/conda-forge/noarch/r-globals-0.19.1-r45hc72bb7e_0.conda#5bb935fc63812c4978f0ac443b8b3420 -https://conda.anaconda.org/conda-forge/osx-64/r-hexbin-1.28.5-r45h5573f66_1.conda#3ca8d4f4595b30f7494ed40aff5a5d40 +https://conda.anaconda.org/conda-forge/osx-64/r-hexbin-1.28.6-r45hf07a639_0.conda#d563c06df380a8e7d6149e78ff975cbc https://conda.anaconda.org/conda-forge/noarch/r-highr-0.12-r45hc72bb7e_0.conda#0b5902d6af02a23bda1794d46090db42 https://conda.anaconda.org/conda-forge/osx-64/r-isoband-0.3.0-r45ha730edb_0.conda#d4a38c5333ebd33cd0443c34bc3ea8f5 https://conda.anaconda.org/conda-forge/noarch/r-lambda.r-1.2.4-r45hc72bb7e_5.conda#0861be0be982bc68a0ec46255331fb63 @@ -230,7 +229,7 @@ https://conda.anaconda.org/conda-forge/osx-64/r-limsolve-2.0.3-r45hf07a639_0.con https://conda.anaconda.org/conda-forge/osx-64/r-matrix-1.7_5-r45h4b87b14_0.conda#778e95b6024b6343cad10290613ee6b8 https://conda.anaconda.org/conda-forge/osx-64/r-modelmetrics-1.2.2.2-r45he949a0c_5.conda#6ec91461eb44dd6fb1bc6eab81345b1f https://conda.anaconda.org/conda-forge/noarch/r-munsell-0.5.1-r45hc72bb7e_2.conda#c78bd534986cde8fc0cb08cc9a1a2cc6 -https://conda.anaconda.org/conda-forge/osx-64/r-nlme-3.1_169-r45hf07a639_0.conda#9317b423f4c264a57a5b81487b7a776b +https://conda.anaconda.org/conda-forge/osx-64/r-nlme-3.1_170-r45hf07a639_0.conda#2efaee95e67ada97a5a4692312c2a9b5 https://conda.anaconda.org/conda-forge/osx-64/r-nnet-7.3_20-r45h735ac91_1.conda#acbe89fcebf4c4340cc96bd2fb019696 https://conda.anaconda.org/conda-forge/osx-64/r-pki-0.1_14-r45h5fa3f5e_3.conda#047ba96e193a7a6aa72b60ee6d436db5 https://conda.anaconda.org/conda-forge/osx-64/r-plyr-1.8.9-r45ha730edb_3.conda#718c137f92edff23c897526d0262c42b @@ -242,13 +241,13 @@ https://conda.anaconda.org/conda-forge/osx-64/r-rcurl-1.98_1.19-r45h0bda0d2_0.co https://conda.anaconda.org/conda-forge/osx-64/r-timechange-0.4.0-r45hed9a748_0.conda#2074adaeb84d5c62b500f556489a26ec https://conda.anaconda.org/conda-forge/noarch/r-tinytex-0.60-r45hc72bb7e_0.conda#5ee226c1449c66d1cd2399d942faa04d https://conda.anaconda.org/conda-forge/osx-64/r-tzdb-0.5.0-r45ha730edb_2.conda#b365065313c3596238f8493331ede8cb -https://conda.anaconda.org/conda-forge/osx-64/r-zip-3.0.0-r45h8eed41d_0.conda#99d64a034e8120d9e507697a366ae892 +https://conda.anaconda.org/conda-forge/osx-64/r-zip-3.0.2-r45h8eed41d_0.conda#9a8543b462d46ca40c9ba29ddb4de761 https://conda.anaconda.org/bioconda/osx-64/bioconductor-biobase-2.70.0-r45h010771c_0.conda#60b5bbcae97d9131ec08f0303d972852 https://conda.anaconda.org/bioconda/osx-64/bioconductor-s4vectors-0.48.0-r45h010771c_1.conda#745c6e80fab9699185df746c1569c889 https://conda.anaconda.org/conda-forge/noarch/r-doparallel-1.0.17-r45hc72bb7e_4.conda#af58987665d786f31bfd45264cb72ae4 https://conda.anaconda.org/conda-forge/osx-64/r-e1071-1.7_17-r45ha730edb_0.conda#ec36aafafa549e7e60b5cf8caac6cc1d https://conda.anaconda.org/conda-forge/noarch/r-futile.logger-1.4.9-r45hc72bb7e_0.conda#3e6624f557885c40a1ea48442734f7e3 -https://conda.anaconda.org/conda-forge/noarch/r-future-1.70.0-r45hc72bb7e_0.conda#aa881360b19ba5911181085679303d5d +https://conda.anaconda.org/conda-forge/noarch/r-future-1.75.0-r45hc72bb7e_0.conda#1bdda0a3f1c032a947cddea3f2b8bc16 https://conda.anaconda.org/conda-forge/noarch/r-gtable-0.3.6-r45hc72bb7e_1.conda#f686123cfba49e6299fae7e029a40266 https://conda.anaconda.org/conda-forge/osx-64/r-htmltools-0.5.9-r45ha730edb_0.conda#cf057b9d43b2b07b4aab30bf9a76b406 https://conda.anaconda.org/conda-forge/noarch/r-knitr-1.51-r45hc72bb7e_0.conda#35b31b96aa7bc052ad6347322a1481f1 @@ -259,7 +258,7 @@ https://conda.anaconda.org/conda-forge/osx-64/r-openxlsx2-1.28-r45h384437d_0.con https://conda.anaconda.org/conda-forge/osx-64/r-proc-1.19.0.1-r45ha730edb_1.conda#cca08d248074ef0c0d61123c863736b5 https://conda.anaconda.org/conda-forge/noarch/r-promises-1.5.0-r45hc72bb7e_1.conda#b2c1b6ef8f12894fd2694b285fe8989a https://conda.anaconda.org/conda-forge/noarch/r-scales-1.4.0-r45hc72bb7e_1.conda#8bc81cc6fd130cef963bc9e082726a14 -https://conda.anaconda.org/conda-forge/osx-64/r-survival-3.8_6-r45hdab4d57_0.conda#ad8052268b3a7fc65dd8f586124b02ef +https://conda.anaconda.org/conda-forge/osx-64/r-survival-3.8_9-r45h8eed41d_0.conda#9cc0a8594d856850fd8ade836cbf78cc https://conda.anaconda.org/conda-forge/osx-64/r-vctrs-0.7.3-r45h384437d_0.conda#b18d1b41722edec3bde565749498800b https://conda.anaconda.org/bioconda/noarch/bioconductor-biocio-1.20.0-r45hdfd78af_0.conda#53e2a6d181467eb5651e4696165763b3 https://conda.anaconda.org/bioconda/osx-64/bioconductor-biocparallel-1.44.0-r45hfbc58e1_1.conda#6888ee4135ca740bf904f40dc97ba4fd @@ -273,7 +272,7 @@ https://conda.anaconda.org/conda-forge/noarch/r-ggplot2-4.0.3-r45h785f33e_0.cond https://conda.anaconda.org/conda-forge/noarch/r-hms-1.1.4-r45hc72bb7e_0.conda#4677c1ad37a9452e27e27d9ed1b8ae90 https://conda.anaconda.org/conda-forge/osx-64/r-httpuv-1.6.16-r45hbf875fd_1.conda#fbf8c73ee9efcb89a7e13db6803f3710 https://conda.anaconda.org/conda-forge/noarch/r-httr-1.4.8-r45hc72bb7e_0.conda#259658089c383f2915b167da3e7890aa -https://conda.anaconda.org/conda-forge/noarch/r-httr2-1.2.3-r45hc72bb7e_0.conda#4b1ea728b72acda530e4e61867acf31f +https://conda.anaconda.org/conda-forge/noarch/r-httr2-1.3.0-r45hc72bb7e_0.conda#b240e3c0e61de35f1f43729f4ea2888e https://conda.anaconda.org/conda-forge/noarch/r-jose-2.0.0-r45hc72bb7e_0.conda#7113381f500ebcc8a33b61101817d120 https://conda.anaconda.org/conda-forge/noarch/r-jquerylib-0.1.4-r45hc72bb7e_4.conda#49a9ed6ed01f4ae6067ead552795bfce https://conda.anaconda.org/conda-forge/noarch/r-pillar-1.11.1-r45hc72bb7e_0.conda#807ef77a70fc5156f830d6c683d07a29 @@ -288,7 +287,7 @@ https://conda.anaconda.org/bioconda/osx-64/bioconductor-s4arrays-1.10.1-r45h0107 https://conda.anaconda.org/bioconda/noarch/bioconductor-seqinfo-1.0.0-r45hdfd78af_0.conda#cfe7c256532f9a4fc87ec3be955bb9e6 https://conda.anaconda.org/bioconda/noarch/bioconductor-ucsc.utils-1.6.1-r45hdfd78af_0.conda#221873955aa526f999e2bb61586e0bbb https://conda.anaconda.org/bioconda/osx-64/bioconductor-xvector-0.50.0-r45h010771c_0.conda#9e213855014249e86b9dc8704aa9b651 -https://conda.anaconda.org/conda-forge/noarch/r-bslib-0.11.0-r45hc72bb7e_0.conda#dae60c429ab933e549832bc223e95639 +https://conda.anaconda.org/conda-forge/noarch/r-bslib-0.12.0-r45hc72bb7e_0.conda#62a97fa00e2f48b594a592dbcbfbe8a5 https://conda.anaconda.org/conda-forge/noarch/r-cowplot-1.2.0-r45hc72bb7e_2.conda#aac95becf98f86e68f344dd2e9a73c12 https://conda.anaconda.org/conda-forge/noarch/r-ggdendro-0.2.0-r45hc72bb7e_2.conda#bcdfec44c6bf587e65f56de61334a413 https://conda.anaconda.org/conda-forge/noarch/r-lava-1.9.2-r45hc72bb7e_0.conda#0bc2bd64e62e0dc086d2173582ffccf3 @@ -325,7 +324,7 @@ https://conda.anaconda.org/bioconda/noarch/bioconductor-summarizedexperiment-1.4 https://conda.anaconda.org/conda-forge/noarch/r-dt-0.34.0-r45hc72bb7e_1.conda#b78224895a1ad7fb52311ab071c2ec00 https://conda.anaconda.org/conda-forge/noarch/r-formattable-0.2.1-r45ha770c72_4.conda#ef91e689156a684857878204973400fb https://conda.anaconda.org/conda-forge/noarch/r-ggalluvial-0.12.6-r45hc72bb7e_0.conda#8a7575b1db70a21d93dd9c7d2c81215a -https://conda.anaconda.org/conda-forge/noarch/r-plotly-4.12.0-r45hc72bb7e_0.conda#ced57d920bed79382f382a24a4425ef7 +https://conda.anaconda.org/conda-forge/noarch/r-plotly-4.12.1-r45hc72bb7e_0.conda#f49a3dafb01430e8e722d6d83be5e52e https://conda.anaconda.org/conda-forge/noarch/r-reactable-0.4.5-r45hc72bb7e_0.conda#125d129980633951a6defcd274537515 https://conda.anaconda.org/conda-forge/noarch/r-recipes-1.3.3-r45hc72bb7e_0.conda#83b25025d6c38b5e341dc96381cd4b6a https://conda.anaconda.org/bioconda/osx-64/bioconductor-genomicalignments-1.46.0-r45h010771c_0.conda#a30b2a6bccd02974024653ceb6071c51 @@ -338,5 +337,5 @@ https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome.hsapiens.ucsc.h https://conda.anaconda.org/bioconda/noarch/bioconductor-bsgenome.hsapiens.ucsc.hg38-1.4.5-r45hdfd78af_4.conda#4baa0dd494a2955755bb00fcd0242f00 https://conda.anaconda.org/bioconda/osx-64/bioconductor-variantannotation-1.56.0-r45h010771c_0.conda#2bc0fa9167469b8ee04400d3b7d3e7f3 https://conda.anaconda.org/bioconda/noarch/bioconductor-mutationalpatterns-3.19.1-r45hdfd78af_0.conda#8a1832a474ae43bb4b015b5a106dbe04 -https://conda.anaconda.org/pcgr/label/dev/noarch/r-pcgrr-2.3.1.9001-h4616a5c_0.conda#b44c3c14e2af1087ad753de83a2a2601 +https://conda.anaconda.org/pcgr/label/dev/noarch/r-pcgrr-2.3.1.9002-h4616a5c_0.conda#a32545b85408dbcb942ffba1c653d5e8 https://conda.anaconda.org/pcgr/label/dev/noarch/r-cpsr-2.2.5.9012-h4616a5c_0.conda#28080c1c508222229783123de6b5e4e7 diff --git a/conda/env/yaml/pcgr.yaml b/conda/env/yaml/pcgr.yaml index 21c2568b..040e36cf 100644 --- a/conda/env/yaml/pcgr.yaml +++ b/conda/env/yaml/pcgr.yaml @@ -6,7 +6,7 @@ channels: - bioconda dependencies: - - pcgr ==2.3.1.9001 # bump + - pcgr ==2.3.1.9002 # bump - bioconda::bedtools - bioconda::bcftools - bioconda::ensembl-vep ==115.1 diff --git a/conda/env/yaml/pcgrr.yaml b/conda/env/yaml/pcgrr.yaml index 839b97f5..e267ff4c 100644 --- a/conda/env/yaml/pcgrr.yaml +++ b/conda/env/yaml/pcgrr.yaml @@ -7,7 +7,7 @@ channels: dependencies: - python - - r-pcgrr ==2.3.1.9001 # bump + - r-pcgrr ==2.3.1.9002 # bump - r-cpsr - r-argparse - bioconductor-bsgenome.hsapiens.ucsc.hg38 diff --git a/conda/env/yaml/pkgdown.yaml b/conda/env/yaml/pkgdown.yaml index f8dd76ea..74bffd4f 100644 --- a/conda/env/yaml/pkgdown.yaml +++ b/conda/env/yaml/pkgdown.yaml @@ -4,7 +4,7 @@ channels: - bioconda - conda-forge dependencies: - - r-pcgrr ==2.3.1.9001 # bump + - r-pcgrr ==2.3.1.9002 # bump - r-pkgdown - r-readr - r-glue diff --git a/conda/recipe/pcgr/recipe.yaml b/conda/recipe/pcgr/recipe.yaml index a15260ab..6774965d 100644 --- a/conda/recipe/pcgr/recipe.yaml +++ b/conda/recipe/pcgr/recipe.yaml @@ -1,6 +1,6 @@ context: name: pcgr - version: 2.3.1.9001 # bump + version: 2.3.1.9002 # bump package: name: ${{ name|lower }} diff --git a/conda/recipe/pcgrr/recipe.yaml b/conda/recipe/pcgrr/recipe.yaml index 5302ea22..e032be4c 100644 --- a/conda/recipe/pcgrr/recipe.yaml +++ b/conda/recipe/pcgrr/recipe.yaml @@ -1,6 +1,6 @@ context: name: r-pcgrr - version: 2.3.1.9001 # bump + version: 2.3.1.9002 # bump package: name: ${{ name|lower }} diff --git a/pcgr/_version.py b/pcgr/_version.py index 60e25a63..3902bb07 100644 --- a/pcgr/_version.py +++ b/pcgr/_version.py @@ -1 +1 @@ -__version__ = '2.3.1.9001' # bump +__version__ = '2.3.1.9002' # bump diff --git a/pcgrr/DESCRIPTION b/pcgrr/DESCRIPTION index 67cb2c13..f83f9b40 100644 --- a/pcgrr/DESCRIPTION +++ b/pcgrr/DESCRIPTION @@ -1,7 +1,7 @@ Package: pcgrr Type: Package Title: Personal Cancer Genome ReporteR -Version: 2.3.1.9001 +Version: 2.3.1.9002 Authors@R: c(person(given = "Sigve", family = "Nakken", diff --git a/pcgrr/NAMESPACE b/pcgrr/NAMESPACE index 42eb1a72..3b3e2a08 100644 --- a/pcgrr/NAMESPACE +++ b/pcgrr/NAMESPACE @@ -164,6 +164,7 @@ export(stats_report_germline) export(stats_report_snv_indel) export(stats_type_snv_indel) export(strip_html) +export(sync_biomarker_evidence) export(tcga_somatic_status) export(tier_af_distribution) export(tmb_doc_note) diff --git a/pcgrr/R/input_data.R b/pcgrr/R/input_data.R index 116dc283..d37a5461 100644 --- a/pcgrr/R/input_data.R +++ b/pcgrr/R/input_data.R @@ -372,6 +372,19 @@ load_somatic_snv_indel <- function( } } + ## Re-sync biomarker evidence items/classifications with the variant set + ## as it stands after all filtering above (allelic depth/fraction, and - + ## for tumor-only input - germline/non-exonic filtering). Biomarker + ## matching was performed once, early, inside load_dna_variants(), against + ## the variant set as it existed prior to this filtering - without this + ## step, evidence items for variants removed above remain orphaned in + ## 'bm_evidence' (see https://github.com/sigven/pcgr/issues/302) + if ("bm_evidence" %in% names(callset)) { + callset[['bm_evidence']] <- sync_biomarker_evidence( + bm_evidence = callset[['bm_evidence']], + var_df = callset[['variant']]) + } + if (NROW(callset[['variant']]) > 0) { callset[['variant']] <- callset[['variant']] |> dplyr::arrange( diff --git a/pcgrr/R/variant_classification.R b/pcgrr/R/variant_classification.R index e3fb72b2..2a65c79e 100644 --- a/pcgrr/R/variant_classification.R +++ b/pcgrr/R/variant_classification.R @@ -281,6 +281,82 @@ assign_amp_asco_cap_tiers <- function( } +#' Re-synchronize biomarker evidence items/classifications with a +#' (possibly further-filtered) variant set +#' +#' Biomarker evidence matching (\code{map_biomarker_data()}, +#' \code{assign_amp_asco_cap_tiers()}) is performed once, early, against +#' the variant set as it existed right after annotation. Callers may go on +#' to remove variants from that set afterwards (e.g. allelic depth/fraction +#' filtering via \code{filter_read_support()}, or germline/non-exonic +#' filtering for tumor-only input). Without re-syncing, evidence items for +#' variants removed by such downstream filtering remain "orphaned" - +#' present in \code{bm_evidence} but absent from the variant set - which +#' surfaces as biomarker-matched variants missing from the variant listing +#' in the report while still appearing in the biomarker evidence listing +#' (see ). +#' +#' @param bm_evidence list with biomarker evidence data (as initialized by +#' \code{init_biomarker_content()}), i.e. top-level 'eitems'/'classification' +#' data frames plus one sub-list per clinical significance category, each +#' with its own 'eitems'/'classification' data frames +#' @param var_df data frame with the final (filtered) variant set +#' +#' @return bm_evidence list, with all 'eitems'/'classification' data frames +#' limited to records matching a variant in var_df +#' +#' @export +sync_biomarker_evidence <- function(bm_evidence = NULL, var_df = NULL) { + + invisible(assertthat::assert_that( + is.list(bm_evidence), + msg = "Argument 'bm_evidence' needs to be of type list")) + invisible(assertthat::assert_that( + is.data.frame(var_df), + msg = "Argument 'var_df' needs to be of type data.frame")) + + join_cols <- intersect( + c("VAR_ID", "VARIANT_CLASS", "ENTREZGENE"), + colnames(var_df)) + + if (length(join_cols) == 0 || NROW(var_df) == 0) { + return(bm_evidence) + } + + variant_keys <- var_df |> + dplyr::select(dplyr::all_of(join_cols)) |> + dplyr::distinct() + + sync_df <- function(df) { + if (is.data.frame(df) && NROW(df) > 0 && + all(join_cols %in% colnames(df))) { + return(dplyr::semi_join(df, variant_keys, by = join_cols)) + } + return(df) + } + + for (elem in c("eitems", "classification")) { + if (elem %in% names(bm_evidence)) { + bm_evidence[[elem]] <- sync_df(bm_evidence[[elem]]) + } + } + + for (clnsig in names(bm_evidence)) { + if (is.list(bm_evidence[[clnsig]]) && + !is.data.frame(bm_evidence[[clnsig]])) { + for (elem in c("eitems", "classification")) { + if (elem %in% names(bm_evidence[[clnsig]])) { + bm_evidence[[clnsig]][[elem]] <- + sync_df(bm_evidence[[clnsig]][[elem]]) + } + } + } + } + + return(bm_evidence) + +} + #' Assign tiers of clinical significance (AMP/ASCO/CAP framework) to #' somatic CNAs #' diff --git a/pcgrr/man/sync_biomarker_evidence.Rd b/pcgrr/man/sync_biomarker_evidence.Rd new file mode 100644 index 00000000..aa7cdcbe --- /dev/null +++ b/pcgrr/man/sync_biomarker_evidence.Rd @@ -0,0 +1,34 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/variant_classification.R +\name{sync_biomarker_evidence} +\alias{sync_biomarker_evidence} +\title{Re-synchronize biomarker evidence items/classifications with a +(possibly further-filtered) variant set} +\usage{ +sync_biomarker_evidence(bm_evidence = NULL, var_df = NULL) +} +\arguments{ +\item{bm_evidence}{list with biomarker evidence data (as initialized by +\code{init_biomarker_content()}), i.e. top-level 'eitems'/'classification' +data frames plus one sub-list per clinical significance category, each +with its own 'eitems'/'classification' data frames} + +\item{var_df}{data frame with the final (filtered) variant set} +} +\value{ +bm_evidence list, with all 'eitems'/'classification' data frames +limited to records matching a variant in var_df +} +\description{ +Biomarker evidence matching (\code{map_biomarker_data()}, +\code{assign_amp_asco_cap_tiers()}) is performed once, early, against +the variant set as it existed right after annotation. Callers may go on +to remove variants from that set afterwards (e.g. allelic depth/fraction +filtering via \code{filter_read_support()}, or germline/non-exonic +filtering for tumor-only input). Without re-syncing, evidence items for +variants removed by such downstream filtering remain "orphaned" - +present in \code{bm_evidence} but absent from the variant set - which +surfaces as biomarker-matched variants missing from the variant listing +in the report while still appearing in the biomarker evidence listing +(see \url{https://github.com/sigven/pcgr/issues/302}). +} diff --git a/pcgrr/vignettes/installation.Rmd b/pcgrr/vignettes/installation.Rmd index 49b07ed6..b9fe0cc2 100644 --- a/pcgrr/vignettes/installation.Rmd +++ b/pcgrr/vignettes/installation.Rmd @@ -15,7 +15,7 @@ require(glue, include.only = "glue") ```{r vars, echo=FALSE} Sys.setenv(VEP_VERSION = "115") -Sys.setenv(PCGR_VERSION = "2.3.1.9001") +Sys.setenv(PCGR_VERSION = "2.3.1.9002") Sys.setenv(BUNDLE_VERSION = "20260620") VEP_VERSION <- Sys.getenv("VEP_VERSION") PCGR_VERSION <- Sys.getenv("PCGR_VERSION") diff --git a/pyproject.toml b/pyproject.toml index 1029c1d3..0fe9b5e8 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -5,7 +5,7 @@ build-backend = "setuptools.build_meta" [project] name = "pcgr" -version = "2.3.1.9001" # bump +version = "2.3.1.9002" # bump description = "Personal Cancer Genome Reporter (PCGR) - variant interpretation for precision cancer medicine" authors = [ {name = "Sigve Nakken", email = "sigven@gmail.com"},