Ecosyste.ms: Issues

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GitHub / iqbal-lab-org/varifier issues and pull requests

#45 - Add option to use mafft

Pull Request - State: closed - Opened by martinghunt about 1 month ago

#44 - Remove global aln indels

Pull Request - State: closed - Opened by martinghunt almost 2 years ago

#43 - Optional homopolymer fix

Pull Request - State: closed - Opened by martinghunt over 2 years ago - 1 comment

#42 - Add option to fix homopolymer indels after MSA

Issue - State: closed - Opened by martinghunt over 2 years ago

#41 - Bug fix gaps at end of global alignment

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

#40 - Skip bcftools norm when using global align method

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

#39 - Only check minimap2 found if using global align

Pull Request - State: closed - Opened by martinghunt over 2 years ago - 1 comment

#38 - A case of a missing `VFR_ED_TR` in precision.vcf

Issue - State: open - Opened by bricoletc over 2 years ago - 1 comment

#37 - make_truth_vcf misses truth SNPs if they lie near dropped amplicons

Issue - State: open - Opened by Danderson123 almost 3 years ago - 3 comments

#36 - Global align output

Pull Request - State: closed - Opened by martinghunt about 3 years ago

#35 - False true-positive

Issue - State: closed - Opened by mbhall88 over 3 years ago - 5 comments

#34 - Add install for conda and containers

Pull Request - State: closed - Opened by mbhall88 over 3 years ago - 1 comment

#33 - Add options --global_align_min_coord, --global_align_max_coord

Pull Request - State: closed - Opened by martinghunt over 3 years ago - 2 comments

#32 - Provide breakdown of variant types

Issue - State: open - Opened by mbhall88 over 3 years ago

#31 - Global align command line option

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

#30 - handle asterisk in non-called alleles

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

#29 - Allele coords in vcf

Pull Request - State: closed - Opened by martinghunt almost 4 years ago

#28 - Indel and N edge cases

Pull Request - State: closed - Opened by martinghunt almost 4 years ago

#27 - New release?

Issue - State: closed - Opened by mbhall88 almost 4 years ago - 6 comments

#26 - Handle non acgt characters

Pull Request - State: closed - Opened by martinghunt almost 4 years ago

#24 - Empty 01.merged.vcf

Issue - State: closed - Opened by jeff-k almost 4 years ago

#23 - Add singularity file and install dependencies script

Pull Request - State: closed - Opened by martinghunt almost 4 years ago - 2 comments

#22 - Bug fixes calling wrong length FP indels as TP

Pull Request - State: closed - Opened by martinghunt almost 4 years ago

#20 - Adding the branch we used in pandora paper

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

#19 - Split ref when running nucmer

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

#18 - Apply variants to probe flanks

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

#17 - Include null as passed FILTER

Issue - State: closed - Opened by mbhall88 over 4 years ago - 3 comments

#16 - Logging formatting and fix header ID

Pull Request - State: closed - Opened by mbhall88 over 4 years ago

#15 - High memory usage

Issue - State: open - Opened by mbhall88 over 4 years ago - 6 comments

#14 - Add ability to read BCF

Issue - State: open - Opened by mbhall88 over 4 years ago - 2 comments

#13 - make bioconda recipe

Issue - State: closed - Opened by mbhall88 over 4 years ago

#12 - add dockerfile

Pull Request - State: closed - Opened by mbhall88 over 4 years ago - 7 comments

#11 - Adding Dockerfile and script to build docker image

Pull Request - State: closed - Opened by leoisl over 4 years ago - 15 comments

#10 - About rev complementing ref and query alleles in dnadiff

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

#9 - Mask truth ref

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

#8 - Edit dist precision recall

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

#7 - Handle conflicting records

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

#6 - Handle asterisk ALTs properly

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

#5 - Add --truth_vcf option

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

#4 - Per record precision as float

Pull Request - State: closed - Opened by martinghunt almost 5 years ago

#3 - make dockerfile

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

#2 - write proper documentation

Issue - State: open - Opened by martinghunt almost 5 years ago - 3 comments

#1 - add travis

Issue - State: open - Opened by martinghunt almost 5 years ago - 3 comments