v0.5.15 (2017-04-28)
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)
Merged pull requests:
v0.5.13 (2017-04-01)
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)
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:
- Add optional_cols list to load_maf #209 (tavinathanson)
v0.5.11 (2016-12-05)
Fixed bugs:
- Varcode noncoding variant in a drop_silent_and_noncoding() list #200
Merged pull requests:
v0.5.10 (2016-10-19)
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)
Fixed bugs:
- StopLoss pickling is broken #188
Closed issues:
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)
Merged pull requests:
v0.5.7 (2016-09-28)
v0.5.3 (2016-09-28)
Merged pull requests:
- Use conda to install pypandoc #189 (arahuja)
- Ensure README.md is packaged #186 (arahuja)
- Upgrade serializable dependency with tests #185 (arahuja)
- Add pypi badge #184 (arahuja)
v0.5.2 (2016-09-28)
Closed issues:
- Make sure
Variantworks 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)
Merged pull requests:
- Add MutationEffect to __init__.py #178 (timodonnell)
v0.5.0 (2016-09-13)
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:
v0.4.19 (2016-09-12)
Fixed bugs:
- original_start doesn't get pickled #141
Closed issues:
- replace
load\_vcfwithload\_vcf\_fast? #144 - Add
annotate\_random\_variantscommandline 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)
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)
Merged pull requests:
v0.4.16 (2016-07-30)
v0.4.15 (2016-07-15)
Fixed bugs:
- Fix clone_with_new_elements for VariantCollection #159 (tavinathanson)
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)
Merged pull requests:
v0.4.12 (2016-05-28)
v0.4.13 (2016-05-28)
Merged pull requests:
v0.4.11 (2016-05-27)
v0.4.10 (2016-05-27)
v0.4.9 (2016-05-27)
Closed issues:
- Add serialization for EffectCollection and VariantCollection #71
Merged pull requests:
v0.4.8 (2016-05-27)
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:
- Modest change to filtering of coding mutations include ExonicSpliceSite #137 (iskandr)
- Version bump #135 (tavinathanson)
- Fix conda install on Travis #134 (iskandr)
- Don't memoize EffectCollection.top_priority_effect() #132 (timodonnell)
- All effects should have a default
short\_descriptionfield #130 (armish) - Remove read_evidence and locus modules #125 (timodonnell)
- Include a link to the iPython notebook in README.md #121 (armish)
- Add varcode to Travis #120 (tavinathanson)
- Minor problem in Variant.__init__ #119 (iskandr)
- Update Varcode to work with new multi-species PyEnsembl #118 (iskandr)
- Fix #116 and call PrematureStop when stop codon is added in the middle of an insertion #117 (leekaiinthesky)
- Warn when variants in MAF file have wrong end position #115 (iskandr)
- Bump pyensembl/varcode version #114 (tavinathanson)
- fix logic for determining whether the protein length decreases #112 (leekaiinthesky)
- decreasing 3' splice site to distance 3 from boundary #109 (iskandr)
- fixed typo in effect inference, added breaking variant to unit tests #108 (iskandr)
- Allow Varcode to work with mouse data via Genome #106 (tavinathanson)
- Manually set compression in read_vcf_into_dataframe #102 (timodonnell)
- Added examples to README #100 (iskandr)
- depend on pandas >= 0.15 #99 (iskandr)
- Faster VCFs loading, support HTTP, and refactored variant metadata #94 (timodonnell)
- Support for regular varcode variant instances in read evidence module #87 (timodonnell)
- Read and write json files #82 (iskandr)
- JSON serialization for VariantCollection. #81 (timodonnell)
- Add short_description field to intergenic variants #80 (timodonnell)
- Speed up PileupCollection.group_by_allele #79 (timodonnell)
- Variant serialization #78 (timodonnell)
- added option for genome name in load_vcf #76 (iskandr)
- Fix variant.effects() to always return an EffectCollection #75 (timodonnell)
- Bump pysam dependency #74 (timodonnell)
- Cufflinks RNA filtering #73 (iskandr)
- Read evidence tweaks #72 (timodonnell)
- Filter effect collection by expression #67 (iskandr)
- Created EpitopeCollection, refactored effects, fix assertion failure while annotating silent stop codon #66 (iskandr)
- Created EpitopeCollection, refactored effects #65 (iskandr)
- include substitution in high priority effects #61 (arahuja)
- don't annotate StopLoss variants that are immediately followed by another stop codon #57 (iskandr)
- Refactor coding effect #55 (iskandr)
- Add read_evidence module #53 (timodonnell)
- Use transcript protein sequence #45 (iskandr)
- Add contributing md #41 (iskandr)
- Small coding effect refactoring and fixes #39 (iskandr)
- Test problematic variants #37 (iskandr)
- Typechecks and test fixes #35 (timodonnell)
- Fix maf parsing #34 (iskandr)
- parse multiple alleles into distinct Variant records #29 (iskandr)
- PEP8 & pyflakes fixes #28 (iskandr)
- Remove pyfaidx #27 (iskandr)
- Variant collection tweaks #24 (timodonnell)
- Improved vcf parsing #23 (timodonnell)
- Associate EnsemblRelease with each Variant object #20 (iskandr)
- Variant collection filtering #19 (iskandr)
- added IntronicSpliceSite, SpliceDonor, SpliceAcceptor effects #17 (iskandr)
- collect effect annotation errors in dictionary, only look up overlapping... #13 (iskandr)
- don't flatten INFO dictionary of VCF, lists are part of the field format #11 (iskandr)
- Small fixes #10 (timodonnell)
- Add support for Python 3 #8 (timodonnell)
- Refactor core logic #7 (iskandr)
- Classes for protein/transcript variant effects #3 (iskandr)
* This Change Log was automatically generated by github_changelog_generator