iqbal-lab-org/cluster_vcf_records issues and pull requests

#50 - Make alleles uppercase and ignore non-ACGT alleles

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

#49 - Vcflib tweaks

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

#48 - Variant tracking: use all alleles

Pull Request - State: closed - Opened by martinghunt about 4 years ago - 1 comment

#47 - Support bcf files

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

#46 - add conda install to docs

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

#45 - include license file when distributing

Pull Request - State: closed - Opened by mbhall88 over 4 years ago - 1 comment

#44 - Add bioconda recipe

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

#43 - Handle different paths in graph that result in same sequence

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

#42 - Improve cluster and merge

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

#41 - Allow adjacent records

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

#40 - Allow adjacent records as per #39

Pull Request - State: closed - Opened by bricoletc about 5 years ago - 2 comments

#39 - Stop clustering adjacent VCF records

Issue - State: open - Opened by bricoletc about 5 years ago - 1 comment

#38 - Ignore VCF records with POS<1 when clustering

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

#37 - GT always printed first in FORMAT if present

Pull Request - State: closed - Opened by martinghunt about 5 years ago - 2 comments

#36 - Fix POS > zero off by one error

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

#35 - General tidying

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

#34 - Clusters not properly extended

Issue - State: closed - Opened by bricoletc over 5 years ago
Labels: bug

#33 - Vcf headers are lost

Issue - State: open - Opened by bricoletc over 5 years ago

#32 - Use filter column

Pull Request - State: closed - Opened by martinghunt almost 6 years ago

#31 - Version bump 0.9.1

Pull Request - State: closed - Opened by martinghunt almost 6 years ago

#30 - Check records match ref seq

Pull Request - State: closed - Opened by martinghunt almost 6 years ago

#29 - total_alleles_lower_bound too low

Pull Request - State: open - Opened by bricoletc about 6 years ago

#28 - Tiny change to try to get travis to build

Pull Request - State: closed - Opened by martinghunt about 6 years ago

#27 - Homozygous bug fix

Pull Request - State: closed - Opened by martinghunt about 6 years ago

#26 - Add GT_CONF to merged alleles

Pull Request - State: closed - Opened by rmcolq about 6 years ago

#25 - Remove bad VCF records

Pull Request - State: closed - Opened by martinghunt over 6 years ago

#24 - Log number of files read

Pull Request - State: closed - Opened by martinghunt over 6 years ago

#23 - Bug fixes testing VCF files correct

Pull Request - State: closed - Opened by martinghunt over 6 years ago

#22 - Lower mem clustering

Pull Request - State: closed - Opened by martinghunt over 6 years ago

#21 - Add gt_aware simple merge feature

Pull Request - State: closed - Opened by rmcolq over 6 years ago

#20 - ValueError raised if VCF contains POS less than 1

Pull Request - State: closed - Opened by ffranr over 6 years ago - 1 comment

#19 - added an alternative single function call interface for vcf clustering; updated README

Pull Request - State: closed - Opened by ffranr over 6 years ago - 1 comment

#18 - Simplified README

Pull Request - State: closed - Opened by ffranr over 6 years ago

#17 - Split records into snps

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#16 - Get sample from file

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#15 - Check empty vcf

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#14 - Version bump 0.3.0

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#13 - Long deletions and many snps

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#12 - Long deletions and many snps

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#11 - Merging at repeats

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#10 - Modified load_vcf_files function to accomodate simple_vcf_merger.

Pull Request - State: closed - Opened by carterjosh almost 7 years ago