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Change Log

v0.5.15 (2017-04-28)

Full Changelog

Closed issues:

  • Allow contig to be empty to allow parsing of MAF with faulty mutation(s) #210

Merged pull requests:

  • Fixes to load_maf #223 (tavinathanson)
  • added raise_on_error option to load_maf and load_maf_dataframe #221 (iskandr)
  • Optionally allow duplicated mutations when using load_vcf or load_maf. Fixes #211 #212 (tuomastik)

v0.5.14 (2017-04-05)

Full Changelog

Merged pull requests:

  • Adding 'distinct' as a parameter to load_vcf. #222 (julia326)

v0.5.13 (2017-04-01)

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Closed issues:

  • Effect prediction throws error (even if raise_on_error=False) #213
  • Optionally allow duplicated mutations when using load_vcf or load_maf #211

Merged pull requests:

  • install ensembl 87 on travis #219 (iskandr)
  • Allow user to affect the sorting of variants when loading a VCF or MAF. #218 (tuomastik)

v0.5.12 (2017-01-18)

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Closed issues:

  • Make Varcode correctly infer genome for b37-decoy string #207
  • Longer indels in random variants #47
  • Predict coding sequence of StartLoss mutations #4

Merged pull requests:

v0.5.11 (2016-12-05)

Full Changelog

Fixed bugs:

  • Varcode noncoding variant in a drop_silent_and_noncoding() list #200

Merged pull requests:

  • Adding aa_ref argument to StopLoss for variants which delete codons before stop #203 (iskandr)

v0.5.10 (2016-10-19)

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Fixed bugs:

  • Variant pickling won't work for not-human and non-EnsemblRelease Genomes #147

Closed issues:

  • Link on PyPI badge broken #191
  • Reference incorrectly inferred when "b36" in reference file path #181
  • Premature stop codon error #166

Merged pull requests:

  • explicit args to __init__ of Intronic splice effects fixes serialization #199 (iskandr)
  • Update RELEASING.md, fixing tagging instructions #198 (julia326)

v0.5.9 (2016-10-11)

Full Changelog

Fixed bugs:

  • StopLoss pickling is broken #188

Closed issues:

  • One logger per module #196
  • SNV results in deletion #193

Merged pull requests:

  • One logger per module. #197 (julia326)
  • Fix edge case where PrematureStop in last amino acid got interpreted as a Deletion #194 (iskandr)
  • Fix inferred-reference-bug #182 (jburos)

v0.5.8 (2016-09-28)

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Merged pull requests:

v0.5.7 (2016-09-28)

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v0.5.3 (2016-09-28)

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Merged pull requests:

v0.5.2 (2016-09-28)

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Closed issues:

  • Make sure Variant works with any Genome (not just a human EnsemblRelease) #127

Merged pull requests:

  • Move extraneous variables to properties for normalization #190 (tavinathanson)
  • Use is_protein_coding property of pyensembl.Transcript and pyensembl.Gene #180 (iskandr)

v0.5.1 (2016-09-16)

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Merged pull requests:

v0.5.0 (2016-09-13)

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Implemented enhancements:

  • Support collection.as_dataframe() #128

Closed issues:

  • Substitution mis-annotated as stop-loss #176
  • Wrong aa_mutation_end_offset for insertion of stop codon #175
  • Wrong aa_ref for insertion of stop codon #174
  • Insertions after the stop codon annotated as plain Insertions #172
  • Mutations before the stop codon confused as StopLosses #171
  • StopLosses do not translate into 3' UTR #170
  • Insertion of stop codon is annotated as simple Insertion and not PrematureStop #169
  • Synonimous FrameShift over stop codon not annotated as silent #168
  • Wrong offset for insertion of StopCodon #167
  • Document release process #154
  • compare variants that use different references #83
  • Annotate with predicted pathogenicity #46

Merged pull requests:

  • Reorganize effect prediction code, fixed annotation bugs/issues #173 (iskandr)

v0.4.19 (2016-09-12)

Full Changelog

Fixed bugs:

  • original_start doesn't get pickled #141

Closed issues:

  • replace load\_vcf with load\_vcf\_fast ? #144
  • Add annotate\_random\_variants commandline script #49
  • support filtering a variant collection to variants overlapping specified gene names #32
  • Use SPANR to identify splicing misregulation #2

v0.4.18 (2016-08-08)

Full Changelog

Closed issues:

  • vcf unit tests broken in python 3 (?) #164
  • maximum recursion depth exceeded when loading a vcf from a URL #163

Merged pull requests:

  • In load_vcf, when passed a URL download it first to a local file then… #165 (timodonnell)
  • Removed Collection from varcode, moved to separate 'sercol' repo instead #162 (iskandr)

v0.4.17 (2016-08-05)

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Merged pull requests:

  • Commandline interface, simplified serialization, merging VariantCollections #161 (iskandr)

v0.4.16 (2016-07-30)

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v0.4.15 (2016-07-15)

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Fixed bugs:

Closed issues:

  • load_vcf_fast fails when sample names contain spaces #158

Merged pull requests:

  • Fix load_vcf_fast for sample names containing a space character #160 (timodonnell)

v0.4.14 (2016-06-07)

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Merged pull requests:

v0.4.12 (2016-05-28)

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v0.4.13 (2016-05-28)

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Merged pull requests:

v0.4.11 (2016-05-27)

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v0.4.10 (2016-05-27)

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v0.4.9 (2016-05-27)

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Closed issues:

  • Add serialization for EffectCollection and VariantCollection #71

Merged pull requests:

  • Reorganized coding effects to use KnownAminoAcidChange base class #153 (iskandr)

v0.4.8 (2016-05-27)

Full Changelog

Fixed bugs:

  • Potentially wrong translated sequence from frameshift on mm10 #151

Closed issues:

  • ExonicSpliceSite mutations are classified as Noncoding #136
  • Filter field is not saved after loading a VCF #89
  • investigate porting read evidence module to use impala #69
  • Attach genotypes and other sample information to Variants #30
  • support determining the evidence for a variant in a bam #26

Merged pull requests:

  • Added unit tests for Klf6 frameshift, fix bug in frameshift translation #152 (iskandr)
  • Add as_dataframe to EffectCollection #150 (arahuja)
  • Use versioneer to manage version number #149 (arahuja)
  • Fix pyvcf error from passing _parse_samples a tuple instead of a list #148 (timodonnell)
  • Fix variant pickling #146 (tavinathanson)
  • Parse and expose sample info, including for multisample VCFs #145 (timodonnell)
  • Preserve contig name #140 (iskandr)
  • Quotes around nucleotides in Variant representation #139 (iskandr)
  • added is_deletion, is_insertion, and is_indel properties to variants #138 (iskandr)

v0.4.2 (2016-02-25)

Implemented enhancements:

  • VariantCollection.high_priority_effect != Variant.top_effect #58
  • Improves the documentation for varcode #110 (armish)
  • Convert effect-type section into a sorted table #104 (armish)
  • Start highlighting Python syntax in README #103 (armish)

Fixed bugs:

  • Varcode requires pandas >= 0.13.1, however it uses 0.15 functionality #12 #92
  • Varcode version 0.3.10 cannot be imported when installed through pip #90
  • pip installing Varcode doesn't seem to work lately #84
  • AttributeError: 'FrameShiftTruncation' object has no attribute 'aa_alt' #70
  • Use find_packages correctly #85 (tavinathanson)

Closed issues:

  • memoize a bit less #131
  • Intragenic variants do not have a short_description field #129
  • move read_evidence module and Locus class to varlens #124
  • Support Structural Variants #122
  • PrematureStop called as Silent #116
  • PrematureStop called as a Deletion #111
  • UnboundLocalError in in_frame_coding_effect.py #107
  • Double mutations in a MAF file cause error #105
  • varcode.load_vcf_fast used 0.16.1 Pandas options #101
  • Configuring datacache default cache directory #98
  • Improve the README to include some examples of working with Varcode in IPython #95
  • support loading VCFs over HTTP #91
  • Travis should include setup.py testing #86
  • Make Variants pickle-able #77
  • modifies_coding_sequence is always false #64
  • AssertionError: aa_ref and aa_alt can't both be empty string #63
  • Too many open files on error on getting top effect #62
  • KeyError: 'reference' in load_vcf #60
  • Issue with n_skip? #56
  • Optional random seed argument for generating random variants #48
  • An argument for using == and not >= for requirements? #43
  • deploy a test coverage tool #38
  • Replace raise_on_error parameter to property of VariantCollection #36
  • assertion error in infer_coding_effect #33
  • add a memoized "highest_priority_effect" property to Variant #31
  • support deep reloading varcode module #25
  • handle multiallelic variants #22
  • vcf.load_vcf should provide an option to load all variants, regardless of whether filter is PASS #21
  • empty variant collection when loading strelka vcf #16
  • Incorrect handling of variants which run past the beginning/end of an exon's boundary #14
  • Reference amino acid sequence sometimes empty for coding variants #12
  • handle single-sample VCFs with INFO fields containing list values of size > 1 #9
  • Do FrameShift (or StopGain) mutations affect splicing? #6
  • What to do with mutations that span the 5' UTR / CDS boundary? #5
  • Annotate essential splice site mutations #1

Merged pull requests:

* This Change Log was automatically generated by github_changelog_generator