Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / ACEnglish/truvari issues and pull requests

#107 - pysam ValueError: start out of range (-1500)

Issue - State: closed - Opened by rlorigro over 2 years ago - 5 comments

#106 - How to merge SV vcfs from different callers?

Issue - State: closed - Opened by xiucz over 2 years ago - 1 comment

#105 - Fix DEL sequence

Pull Request - State: closed - Opened by wwliao over 2 years ago - 2 comments

#104 - Fix mixed types in remaining calls

Pull Request - State: closed - Opened by wwliao over 2 years ago

#103 - Fix genotype consolidation

Pull Request - State: closed - Opened by wwliao over 2 years ago

#101 - Truvari giving incorrect vcf format error

Issue - State: closed - Opened by aditya-sarkar441 over 2 years ago - 7 comments

#100 - VCF format error

Issue - State: closed - Opened by Addicted-to-coding over 2 years ago - 3 comments

#98 - explainantion on --gtcomp and genotype concordance

Issue - State: closed - Opened by prasundutta87 almost 3 years ago - 8 comments

#97 - ZeroDivisionError in /truvari/bench.py

Issue - State: closed - Opened by stefmldk almost 3 years ago - 1 comment

#91 - No true positives being found on some chromosomes

Issue - State: closed - Opened by fbursa almost 3 years ago - 5 comments

#90 - An error when used melt's SV result in truvari

Issue - State: closed - Opened by rescuz almost 3 years ago - 1 comment

#89 - Low precision when using wf-human-sv

Issue - State: closed - Opened by imdanique almost 3 years ago - 1 comment

#88 - Incorrect results with multi-allelic records

Issue - State: closed - Opened by ldenti about 3 years ago - 1 comment

#85 - Extend bench FP annotation.

Issue - State: closed - Opened by ACEnglish about 3 years ago
Labels: enhancement

#84 - Error while running Truvari

Issue - State: closed - Opened by prasundutta87 about 3 years ago - 9 comments

#81 - Remove redundant code

Pull Request - State: closed - Opened by wwliao about 3 years ago - 1 comment

#80 - git clone doesn't work git-lfs smudge

Issue - State: closed - Opened by MeHelmy about 3 years ago - 1 comment

#79 - Fix if condition

Pull Request - State: closed - Opened by wwliao about 3 years ago - 1 comment

#75 - Truvari running errors from Parliament2

Issue - State: closed - Opened by daft-punkk over 3 years ago - 2 comments

#74 - GIAB Report Support type not coming up

Issue - State: closed - Opened by stanleyrc over 3 years ago - 2 comments

#73 - Create CODE_OF_CONDUCT.md

Pull Request - State: closed - Opened by ACEnglish over 3 years ago

#72 - Compatibility with GRIDSS output

Issue - State: closed - Opened by stanleyrc over 3 years ago - 1 comment

#71 - problem for using truvari

Issue - State: closed - Opened by azure-twilight over 3 years ago - 3 comments

#70 - Unable to parse comparison vcf file

Issue - State: closed - Opened by wjj666 over 3 years ago - 1 comment

#69 - python-levenshtein: 0.12.1 -> 0.12.2

Pull Request - State: closed - Opened by scalavision over 3 years ago - 1 comment

#68 - truset file as bed

Issue - State: closed - Opened by Manuelaio over 3 years ago - 1 comment

#67 - Relatively low performance on different SV size

Issue - State: closed - Opened by SQLiu-youyou over 3 years ago - 1 comment

#66 - can truvari evaluate vcfs on haplotype level

Issue - State: closed - Opened by yekaizhou over 3 years ago - 1 comment

#65 - cannot install using conda

Issue - State: closed - Opened by yekaizhou over 3 years ago - 2 comments

#64 - --help is inaccurate

Issue - State: closed - Opened by InvisOn over 3 years ago - 1 comment

#63 - simple fix to README

Issue - State: closed - Opened by RichardCorbett almost 4 years ago - 1 comment

#62 - Check Base.vcf.gz[.tbi]

Issue - State: closed - Opened by ACEnglish almost 4 years ago
Labels: enhancement

#61 - Add Deployed Documentation Link

Pull Request - State: closed - Opened by sonny-mo almost 4 years ago - 1 comment

#59 - template not working properly

Issue - State: closed - Opened by scalavision about 4 years ago - 3 comments

#57 - Truvari does not recognize call in base VCF

Issue - State: closed - Opened by botcricket about 4 years ago - 1 comment

#56 - ‘Mismatch when double-checking Truvari calculations

Issue - State: closed - Opened by shengbing about 4 years ago - 2 comments

#55 - truvari does not support variants in BND notation.

Issue - State: closed - Opened by d-cameron over 4 years ago - 2 comments

#54 - Error: values expected to be 2-tuple, given len=1

Issue - State: closed - Opened by cjain7 over 4 years ago - 1 comment

#53 - Revert "Bump progressbar2 dependency version"

Pull Request - State: closed - Opened by ACEnglish over 4 years ago

#52 - Bump progressbar2 dependency version

Pull Request - State: closed - Opened by turion over 4 years ago

#51 - No 2.0 Tag

Issue - State: closed - Opened by WEClarke over 4 years ago - 3 comments

#50 - KeyError: 'Illcalls'

Issue - State: closed - Opened by AYYYang over 4 years ago - 1 comment

#48 - Usable VCF

Issue - State: closed - Opened by ACEnglish over 4 years ago
Labels: enhancement

#47 - Potential typo in get_vcf_variant_type()

Issue - State: closed - Opened by eldariont over 4 years ago - 1 comment

#46 - setup.py exact dependency versions

Issue - State: closed - Opened by KoviRobi over 4 years ago - 1 comment

#45 - Truvari not adding variants to call count or interval tree for comparsion.

Issue - State: closed - Opened by gorupria almost 5 years ago - 1 comment

#43 - TypeError: values expected to be 1-tuple, given len=2

Issue - State: closed - Opened by Tintest almost 5 years ago - 3 comments

#42 - What does 'sequence resolved calls' mean?

Issue - State: closed - Opened by gorupria almost 5 years ago - 1 comment

#41 - [E::get_intv] Failed to parse TBX_GENERIC, was wrong -p [type] used?

Issue - State: closed - Opened by shengbing almost 5 years ago - 2 comments

#40 - TypeError: '>=' not supported between instances of 'int' and 'NoneType'

Issue - State: closed - Opened by shengbing almost 5 years ago - 1 comment

#39 - TypeError: '>=' not supported between instances of 'int' and 'NoneType'

Issue - State: closed - Opened by shengbing almost 5 years ago - 1 comment

#38 - Error parsing SVLEN=.

Issue - State: closed - Opened by johnemajor almost 5 years ago - 1 comment

#37 - Running on same CNV VCF file yields no results?

Issue - State: closed - Opened by johnemajor about 5 years ago - 2 comments

#36 - AttributeError: 'IntervalTree' object has no attribute 'search'

Issue - State: closed - Opened by johnemajor about 5 years ago - 2 comments

#35 - Truvari 1.3.4 freezes during analysis of DELLY results

Issue - State: closed - Opened by ofonov about 5 years ago - 2 comments

#34 - Question regarding matching parameters

Issue - State: closed - Opened by ofonov about 5 years ago - 1 comment

#33 - ValueError: 'pysam.libcbcf.VariantFile.fetch' requires an index

Issue - State: closed - Opened by tjiangHIT about 5 years ago - 5 comments

#32 - Truvari v1.2 and v1.3.2 give different results

Issue - State: closed - Opened by sjurug about 5 years ago - 7 comments

#31 - Bug Fix: Cannot sort list with 'pysam.libcbcf.VariantRecord' element

Pull Request - State: closed - Opened by caspargross about 5 years ago - 1 comment

#30 - AttributeError: 'pysam.libcbcf.VariantFile' object has no attribute 'contigs'

Issue - State: closed - Opened by caspargross about 5 years ago - 2 comments

#7 - Strict comparison should always return a subset of loose comparison.

Issue - State: closed - Opened by ACEnglish over 6 years ago - 3 comments
Labels: bug, enhancement