brentp/echtvar issues and pull requests

#45 - '.' missing value placeholder

Issue - State: open - Opened by davidfstein 9 days ago

#44 - error when encoding gnomad 4.1 vcf

Issue - State: closed - Opened by atimms about 2 months ago - 2 comments

#43 - Missing Number= with gnomad.v3.1.2.echtvar.v2.zip

Issue - State: closed - Opened by fellen31 3 months ago - 6 comments

#42 - Update CADD link and warn about licensing requirements

Pull Request - State: closed - Opened by dvg-p4 4 months ago

#41 - Unsupported Field Type: Flag

Issue - State: closed - Opened by Fyodir 7 months ago - 1 comment

#40 - Filter Echtvar annotated VCF

Issue - State: open - Opened by kcygan 9 months ago

#39 - Feature/fix issue 36

Pull Request - State: closed - Opened by migbro 10 months ago - 7 comments

#38 - 🔧 description testing updates

Pull Request - State: closed - Opened by dmiller15 10 months ago

#37 - non ACGT Bug fix kinda

Pull Request - State: closed - Opened by migbro 10 months ago - 6 comments

#36 - 🐛 non ACGT ALT character

Issue - State: closed - Opened by migbro 10 months ago - 10 comments

#35 - ✨ scrape descriptions on encode

Pull Request - State: closed - Opened by dmiller15 10 months ago - 6 comments

#34 - 🔨 Scrape Number and Specify Description

Pull Request - State: closed - Opened by migbro 10 months ago - 4 comments

#33 - Feature Request: Port/Add Description

Issue - State: closed - Opened by migbro 10 months ago - 2 comments

#32 - 🐛 report BCF2 missing floats

Pull Request - State: closed - Opened by dmiller15 about 1 year ago - 2 comments

#32 - 🐛 report BCF2 missing floats

Pull Request - State: closed - Opened by dmiller15 about 1 year ago - 2 comments

#30 - error om encoding dbsnp - "Large file option has not been set". echtvar 0.1.7

Issue - State: closed - Opened by ruslan-abasov about 1 year ago - 3 comments

#29 - Help message for echtvar anno should call the arg <OUTPUT_BCF>, not <OUTPUT_VCF>

Issue - State: closed - Opened by dvg-p4 over 1 year ago - 3 comments

#28 - -1 as a default missing value does not work when the actual annotation value could be -1

Issue - State: closed - Opened by dvg-p4 over 1 year ago - 12 comments

#27 - Fix vcf header in cadd2vcf.py

Pull Request - State: closed - Opened by dvg-p4 over 1 year ago - 1 comment

#26 - encode error

Issue - State: open - Opened by cheanney over 1 year ago - 1 comment

#25 - Typos

Pull Request - State: closed - Opened by enormandeau over 1 year ago - 1 comment

#24 - static binary

Issue - State: closed - Opened by jianshu93 about 2 years ago - 6 comments

#23 - position mistake of warning?:`[warning] found non ACGT ALT character 'N', encoding as 'T' for position: 1547942`

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

#22 - warn for VCFv4.2:[warning] found non ACGT ALT character '*', encoding as 'T' for position: 774922

Issue - State: closed - Opened by liserjrqlxue over 2 years ago - 11 comments

#21 - Echtvar slower on VCF with many samples

Issue - State: closed - Opened by edg1983 over 2 years ago - 2 comments

#20 - dbsnp and multiallelic VCFs

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

#19 - INFO field header key order

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

#18 - [bugfix] Fix MacOS builds

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

#17 - Running on MacOS

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

#16 - [bugfix] Fix handling of ref-only records in VCF

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

#15 - dbnsfp script - output minimum for certain values

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

#14 - Encode TSV indexed files

Issue - State: closed - Opened by edg1983 over 2 years ago - 2 comments

#13 - allow string (constants) in expressions

Issue - State: open - Opened by brentp over 2 years ago

#12 - index out of range when encoding large VCF

Issue - State: closed - Opened by JakeHagen almost 3 years ago - 9 comments

#11 - Multi-allelic sites

Issue - State: closed - Opened by m-pauper almost 3 years ago - 4 comments

#10 - Multiplier for float

Issue - State: closed - Opened by m-pauper almost 3 years ago - 3 comments

#9 - Kernel too old

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

#8 - thread 'main' panicked at 'index out of bounds

Issue - State: closed - Opened by davetang almost 3 years ago - 6 comments

#7 - Categories

Pull Request - State: closed - Opened by brentp almost 3 years ago

#6 - sanitize alias

Issue - State: open - Opened by brentp almost 3 years ago

#5 - Fix anno usage

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

#4 - use thin_vec for larger variants

Issue - State: open - Opened by brentp almost 3 years ago - 1 comment
Labels: enhancement

#3 - allow extracting and annotating with FILTER field and with flags

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

#2 - support multiple echtvar files

Issue - State: closed - Opened by brentp almost 3 years ago

#1 - handle 'chr21' vs '21'

Issue - State: closed - Opened by brentp almost 3 years ago

GitHub / brentp/echtvar issues and pull requests