Production
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copy_number_plotter

Public
  1. Production
  2. copy_number_plotter

Commits

AuthorCommitMessageCommit dateIssues
Dustin BleileDustin Bleile
57311418307MPull request #45: Release/v1.3.0 CLININFO-747 heatmap plotter updateMerge in PROD/copy_number_plotter from release/v1.3.0_CLININFO-747_heatmap_plotter_update to master * commit 'ba392a269803fd8f974534fb40f735b5df689af3': v1.3.0 - setup.py - numpy<2.4 - prevent TypeError: only 0-dimensional arrays can be converted to Python scalars Release v1.3.0 - heatmap plotter updates New Features: * heatmap plotter - still make an image (with nothing on it) for when d...CLININFO-747
Dustin BleileDustin Bleile
ba392a26980v1.3.0 - setup.py - numpy<2.4 - prevent TypeError: only 0-dimensional arrays can be converted to Python scalars
Dustin BleileDustin Bleile
003bb42d07dRelease v1.3.0 - heatmap plotter updatesNew Features: * heatmap plotter - still make an image (with nothing on it) for when data are outside of the programmed limits * heatmap plotter - extras which will be used for an ML classifier for TC/ploidy and noisy samples: 1. minimal heatmap 2. csv file with normalized data (bins) 3. csv file with normalized data (zoned)
John DupuisDustin BleileJohn Dupuis
233df893313MPull request #44: CLININFO-747.heatmap plotter updatesMerge in PROD/copy_number_plotter from heatmap_rerun_fix to develop * commit '7a15a38fd5879c46f4cf65816d60e0d1af46c73e': CLININFO-747.heatmap plotter updatesCLININFO-747
Dustin BleileDustin Bleile
7a15a38fd58MMerge branch 'develop' of https://svn.bcgsc.ca/bitbucket/scm/prod/copy_number_plotter into heatmap_rerun_fix
Dustin BleileDustin Bleile
eb5129fb0adcentos7 scipy<=1.16.3 - for numpy version compatibility
John DupuisJohn Dupuis
d87f8da78c7CLININFO-747.heatmap plotter updatesCLININFO-747
Dustin BleileDustin Bleile
99bf2232699MPull request #43: Release/v1.2.2 CLININFO-747 bugfix off axix dataMerge in PROD/copy_number_plotter from release/v1.2.2_CLININFO-747_bugfix_off-axix_data to master * commit '0383e91a2cf8394c3ee2f8d4578177f02679e0f3': Release v1.2.2 Bugfixes: * CLININFO-747 - Sometimes the plotter plots data off-axis Improvements: * CLININFO-747 - updated some of the slicing of data for efficiency & remove duplication lint - trivial CLININFO-747.fixed y limits used fo...CLININFO-747
Dustin BleileDustin Bleile
0383e91a2cfRelease v1.2.2Bugfixes: * CLININFO-747 - Sometimes the plotter plots data off-axis Improvements: * CLININFO-747 - updated some of the slicing of data for efficiency & remove duplicationCLININFO-747
John DupuisDustin BleileJohn Dupuis
26e897dd5b7MPull request #42: CLININFO-747.bugfix; off-axis dataMerge in PROD/copy_number_plotter from off-axis_data_fix to develop * commit '0fca0a40e50abb54dca35404e08752ce5e6ac7c8': lint - trivial CLININFO-747.fixed y limits used for CNV parsing CLININFO-747.bugfix; off-axis dataCLININFO-747
Dustin BleileDustin Bleile
0fca0a40e50lint - trivial
Dustin BleileDustin Bleile
7f740d19934MMerge branch 'develop' of https://svn.bcgsc.ca/bitbucket/scm/prod/copy_number_plotter into off-axis_data_fix
John DupuisJohn Dupuis
2c89aa29ae7CLININFO-747.fixed y limits used for CNV parsingCLININFO-747
John DupuisJohn Dupuis
e6844f3b9f4CLININFO-747.bugfix; off-axis dataCLININFO-747
Dustin BleileDustin Bleile
ff836a39bbaMPull request #41: Release/v1.2.1 SDEV-5194 log missing sageMerge in PROD/copy_number_plotter from release/v1.2.1_SDEV-5194_log_missing_sage to master * commit '3af08584b6805e8f5e99c8c6033da5f8fbb20165': release v1.2.1 - Makefile - update dist - isolated build only - do not call install Release v1.2.1 Improvements: * SDEV-5194 - check and log missing sage / purity files * SDEV-5194 - fix tests - update test data to use purple.cnv.somatic.loh.t...2 Jira issues
Dustin BleileDustin Bleile
3af08584b68release v1.2.1 - Makefile - update dist - isolated build only - do not call install
Dustin BleileDustin Bleile
37f766f596bRelease v1.2.1Improvements: * SDEV-5194 - check and log missing sage / purity files * SDEV-5194 - fix tests - update test data to use purple.cnv.somatic.loh.tsv * SDEV-5194 - skip tests on bamboo - no file accessSDEV-5194
Dustin BleileDustin Bleile
a74745b6184MPull request #40: Feature/SDEV-5194 crash on purple no sageMerge in PROD/copy_number_plotter from feature/SDEV-5194_crash_on_purple_no_sage to develop * commit '2d2b7e74fb6e879a75229a2c5518892dad9ab40e': SDEV-5194 - skip tests on bamboo - no file access SDEV-5194 - skip tests on bamboo - no file access SDEV-5194 - update tests SDEV-5194 - fix tests - update test data to use purple.cnv.somatic.loh.tsv SDEV-5194 - fix typing - Path of None t...SDEV-5194
Dustin BleileDustin Bleile
2d2b7e74fb6SDEV-5194 - skip tests on bamboo - no file accessSDEV-5194
Dustin BleileDustin Bleile
aaf346b016eSDEV-5194 - skip tests on bamboo - no file accessSDEV-5194
Dustin BleileDustin Bleile
7e7449c3eaeSDEV-5194 - update testsSDEV-5194
Dustin BleileDustin Bleile
174b8cc4dd9SDEV-5194 - fix tests - update test data to use purple.cnv.somatic.loh.tsvSDEV-5194
Dustin BleileDustin Bleile
9da1fd6bef0SDEV-5194 - fix typing - Path of NoneSDEV-5194
Dustin BleileDustin Bleile
ca3d56dd29dtype fixes
Dustin BleileDustin Bleile
9da89695c7cSDEV-5194 - check missing sage / purity filesSDEV-5194
Dustin BleileDustin Bleile
4f80aaf072dSDEV-4994 - Makefile - fix upload sectionSDEV-4994
Dustin BleileDustin Bleile
dbba73bd96cMPull request #38: Release/v1.2.0 CLININFO-747 SDEV-5075Merge in PROD/copy_number_plotter from release/v1.2.0_CLININFO-747_SDEV-5075 to master * commit 'b91e9b20330a63065cb11753f148352a46184e71': Release v1.2.0 New Features: * CLININFO-747 - updated LOH coloring * SDEV-5075 - rocky9 compatible installation & run CLININFO-747.circos loh updates SDEV-5075 - process_AF.sh - rocky9 bcftools-1.19/bin/bcftools SDEV-5075 - process_AF.sh - bedtoo...3 Jira issues
Dustin BleileDustin Bleile
b91e9b20330Release v1.2.0New Features: * CLININFO-747 - updated LOH coloring * SDEV-5075 - rocky9 compatible installation & run2 Jira issues
Dustin BleileDustin Bleile
af50ef8b455MPull request #37: Feature/SDEV-5075 rocky9 compatible installMerge in PROD/copy_number_plotter from feature/SDEV-5075_rocky9_compatible_install to develop * commit '07999991d3192332e9b907395cfaa970d3bc0e5b': SDEV-5075 - process_AF.sh - rocky9 bcftools-1.19/bin/bcftools SDEV-5075 - process_AF.sh - bedtools & bcftools path from /etc/os-release to distinguish rocky9 from centos7 SDEV-5075 - simplify imports SDEV-5075 - fix typesSDEV-5075
Dustin BleileDustin Bleile
07999991d31MMerge branch 'develop' of https://svn.bcgsc.ca/bitbucket/scm/prod/copy_number_plotter into feature/SDEV-5075_rocky9_compatible_installSDEV-5075
John DupuisDustin BleileJohn Dupuis
063bcfbbb34MPull request #35: CLININFO-747.update LOH parsingMerge in PROD/copy_number_plotter from update_loh to develop * commit 'ea65367a67a8a50a52c00e93fe63a3d0d6c82522': CLININFO-747.circos loh updates SDEV-5075 - fix types lint - remove unused imports CLININFO-747 - bugfix cmaps call SDEV-5075 - Makefile setup.py - centos7 build dependencies added CLININFO-747.reconciling branches CLININFO-747.update LOH parsing2 Jira issues
Dustin BleileDustin Bleile
d9fcf2af6ddMMerge branch 'update_loh' of https://svn.bcgsc.ca/bitbucket/scm/prod/copy_number_plotter into feature/SDEV-5075_rocky9_compatible_installSDEV-5075
John DupuisJohn Dupuis
ea65367a67aCLININFO-747.circos loh updatesCLININFO-747
Dustin BleileDustin Bleile
ddf282f7193SDEV-5075 - process_AF.sh - rocky9 bcftools-1.19/bin/bcftoolsSDEV-5075
Dustin BleileDustin Bleile
8fa17f635dcSDEV-5075 - process_AF.sh - bedtools & bcftools path from /etc/os-release to distinguish rocky9 from centos7SDEV-5075
Dustin BleileDustin Bleile
ebef049c2edSDEV-5075 - simplify importsSDEV-5075
Dustin BleileDustin Bleile
8598da7de78SDEV-5075 - fix typesSDEV-5075
Dustin BleileDustin Bleile
167b6d08d4aSDEV-5075 - fix typesSDEV-5075
Dustin BleileDustin Bleile
823826bbceblint - remove unused imports
Dustin BleileDustin Bleile
2840332f562CLININFO-747 - bugfix cmaps callCLININFO-747
Dustin BleileDustin Bleile
1d08e46ff1eSDEV-5075 - Makefile setup.py - centos7 build dependencies addedSDEV-5075
John DupuisJohn Dupuis
34bdf7fc804CLININFO-747.reconciling branchesCLININFO-747
John DupuisJohn Dupuis
1e63349747eMCLININFO-747.reconciling branchesCLININFO-747
John DupuisJohn Dupuis
50eb388d327CLININFO-747.update LOH parsingCLININFO-747
Dustin BleileDustin Bleile
0c8a30a8faeMPull request #34: Bugfix/SDEV-5035 heatmap crash w purity min maxMerge in PROD/copy_number_plotter from bugfix/SDEV-5035_heatmap_crash_w_purity_min_max to develop * commit 'ca720fb40f378a10764da90fcaca9d57945d43ac': lint - unused import SDEV-5035 - process_ploidetect_bins - rint on data_copies SDEV-5075 - fix test_process_ploidetect_bins2 Jira issues
Dustin BleileDustin Bleile
ca720fb40f3lint - unused import
Dustin BleileDustin Bleile
4bddb833c12SDEV-5035 - process_ploidetect_bins - rint on data_copiesSDEV-5035
Dustin BleileDustin Bleile
8dbef866beaSDEV-5075 - fix test_process_ploidetect_binsSDEV-5075
Dustin BleileDustin Bleile
3772f619c88MPull request #33: Release/v1.1.1 CLININFO-747 color updatesMerge in PROD/copy_number_plotter from release/v1.1.1_CLININFO-747_color_updates to master * commit 'f6200c6cec8a43dcf723de5c461ea7de41ad2b78': Release v1.1.1 Bugfix: * SDEV-5022 - PASS VAFs always zero unless editable pip install location used. Improvements: * CLININFO-747 - update copy color assignment for plotters - use int(copies) to match IPR SDEV-5022 - bugfix - PASS VAFs always ze...2 Jira issues
Dustin BleileDustin Bleile
f6200c6cec8Release v1.1.1Bugfix: * SDEV-5022 - PASS VAFs always zero unless editable pip install location used. Improvements: * CLININFO-747 - update copy color assignment for plotters - use int(copies) to match IPR2 Jira issues