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Commits on Mar 29, 2019

• New 'bintest' command superseding cnv_ztest.py script

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Commits on Mar 22, 2019

• Remove all Python 2.7 compatibility shims

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Commits on Mar 20, 2019

• Replace pd.read_table with pd.read_csv(sep='\t')

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Commits on Jun 28, 2018

• cnv_annotate.py: bugfix (etal#367)

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Commits on Jun 20, 2018

• scripts/snpfilter.sh: Handle optional argument 'fasta' (etal#364)

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Commits on Jun 15, 2018

• Add snpfilter.sh to help create usable T/N VCFs

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Commits on Jun 8, 2018

• ztest: Moved functions from script to new module

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Commits on Jun 6, 2018

• cnv_expression_correlate.py: Avoid a crash on Py3

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Commits on Feb 23, 2018

• Cleanup: comments & whitespace

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Commits on Feb 22, 2018

• coverage, guess_baits: Deal better with BED + extra columns (etal#301)

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Commits on Feb 21, 2018

• skg_convert.py: Add options for feature parity with refFlat2bed.py (etal#311)

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Commits on Feb 15, 2018

• skg_convert.py: Add stub options for GFF parsing (etal#311)

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Commits on Jan 30, 2018

• scripts: Clarify options (etal#301)

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Commits on Jan 25, 2018

• Add '--haploid-x-reference' as an alias for '--male-reference'

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Commits on Jan 12, 2018

• Replace np.asarray(pd.Series) with pd.Series.values

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Commits on Jan 10, 2018

• Roll import_* scripts into new command 'import-rna'

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Commits on Dec 7, 2017

• rna: Split CNV-expression correlation calculation into separate script

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Commits on Dec 1, 2017

• Add 2 scripts to infer copy number from RNA expression

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Commits on Nov 9, 2017

• Remove deprecated script refFlat2bed.py. (Use skg_convert.py instead.)

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Commits on Oct 16, 2017

• scripts: Rename "cn_*.py" to "cnv_*.py"

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• cn_updater.py: Also rename "Background" bins to "Antitarget"

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Commits on Sep 16, 2017

• scripts/cn_ztest.py: Adjust p-values for 2-sided testing

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Commits on Sep 15, 2017

• scripts/cn_ztest.py: Options to account for known segs, sex chroms

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• scripts: Rename "cnn_*.py" to "cn_*.py"

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• Add script cn_ztest.py to detect single-exon CNAs

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Commits on Aug 17, 2017

• doc: Update descriptions of scripts

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Commits on Apr 18, 2017

• scripts: Add cn_annotate.py (WIP)

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• scripts: Add skg_convert.py

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Commits on Mar 6, 2017

• Move tabio sub-package from cnvlib to skgenome (etal#201)

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• Remove script coverage_bin_size.py

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Commits on Feb 25, 2017

• Add 'autobin' command, based coverage_bin_size.py (closes etal#170)

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Commits on Jan 6, 2017

• guess_baits: In unguided scan, trim target edges to 1/2 target peak.

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Commits on Jan 3, 2017

• New script guess_baits.py (WIP)

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Commits on Jan 2, 2017

• samutil: rename bam_read_counts -> idxstats

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Commits on Jan 1, 2017

• New module 'autobin' extracted from script coverage_bin_size.py

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