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Commits on Feb 24, 2023

• test: Fix Makefile to use the installed cnvkit.py instead of local paths

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• test: Apply black and pylint to test runner scripts

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Commits on Feb 22, 2023

• Use pytest in tox.ini and test/Makefile

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• test: Add conftest.py to make pytest work properly

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• test: fix bit rot so unit tests pass cleanly

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Commits on Feb 25, 2022

• Added variables for 'rscript' and 'python'

  

  Felix VDM

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Commits on Feb 22, 2022

• test: Add example BED file with Agilent-style 2-line header

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Commits on Nov 12, 2019

• test: silence DeprecationWarning during unit tests

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Commits on Nov 11, 2019

• Modification of Build files , removing MAc with pyhton 3.5 (unable to install DNA copy and provisionaly commenting out one 1 test on test_commands.py that fails the build (needs looking into at a l…

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  duartemolha

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Commits on Apr 15, 2019

• test/test_r.py: Silence the internal log messages, like the other tests

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• Use iterative SG smoothing with a narrow bandwidth

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Commits on Apr 12, 2019

• segment hmm: Fix a bug where segment endpoints could be scrambled

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• Fixes

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Commits on Apr 11, 2019

• batch: Do segmetrics/call/bintest post-processing here.

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Commits on Apr 9, 2019

• segmetrics: Implement & expose --smooth-bootstrap option

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• scatter: Use a safe matplotlib backend on OS X to avoid crash

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• Silence warnings in pysam and pomegranate that we can't control

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Commits on Mar 31, 2019

• segmetrics: Add 'ttest' option for 1-sample t-test p-value

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Commits on Mar 29, 2019

• New 'bintest' command superseding cnv_ztest.py script

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Commits on Mar 28, 2019

• reference, fix: Implement --cluster (closes etal#308)

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Commits on Mar 22, 2019

• Remove all Python 2.7 compatibility shims

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Commits on Mar 21, 2019

• batch, segment: Remove deprecated option --rlibpath

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Commits on Mar 20, 2019

• test: Improve unit tests for 'target' command

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• test: Replicate 'scatter -c chr21' indexing issue (etal#393)

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• Fix a VCF parsing warning

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Commits on Mar 1, 2019

• travis, docker, conda: Remove cghFLasso dependency (etal#419)

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Commits on Nov 3, 2018

• vcfio: support GATK inputs with empty ALT alleles

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  chapmanb

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Commits on Jul 8, 2018

• iter_slices: Respect keep_empty the same way as by_ranges

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Commits on Jul 3, 2018

• skgenome: fix iter_slices, iter_ranges_of, intersection

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Commits on Jun 30, 2018

• GA: add 'intersection' method (closes etal#340)

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Commits on Jun 11, 2018

• segmetrics: streamline & optimize (etal#346)

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Commits on Mar 2, 2018

• segmetrics, genemetrics: Make list-type args default to [] (etal#325)

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Commits on Jan 20, 2018

• segmetrics: Move supporting functions to a new module

  etal

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Commits on Jan 19, 2018

• Rename 'gainloss' command to 'genemetrics' (etal#278)

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Commits on Jan 13, 2018

• Merge branch 'master' of github.com:etal/cnvkit

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