Ecosyste.ms: Issues

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GitHub / amplab/smash issues and pull requests

#25 - Bump junit from 4.11 to 4.13.1 in /calldiff

Pull Request - State: open - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#24 - Upgrade genomics version to match GA4GH v0.5.1

Pull Request - State: closed - Opened by cassiedoll almost 10 years ago

#23 - Adds the --nolocalserver flag and supporting authentication flow

Pull Request - State: closed - Opened by mbookman almost 10 years ago

#22 - Enable command line specification of VCF files or callsetIds

Pull Request - State: closed - Opened by chapmanb about 10 years ago - 2 comments

#21 - Kelly's super cool java program for comparing variant sets

Pull Request - State: closed - Opened by kwestbrooks about 10 years ago

#20 - output stats in JSON

Issue - State: closed - Opened by jn80842 about 10 years ago - 1 comment
Labels: enhancement

#19 - standardize output stats

Issue - State: closed - Opened by jn80842 about 10 years ago - 1 comment

#18 - compare bases case-insensitively

Issue - State: closed - Opened by jn80842 about 10 years ago - 1 comment

#17 - output vcf file discards original INFO field

Issue - State: closed - Opened by jn80842 about 10 years ago - 1 comment

#16 - error rates should be in proportion to variant category

Issue - State: closed - Opened by jn80842 about 10 years ago - 1 comment

#15 - SMaSH uses too much memory

Issue - State: closed - Opened by jn80842 about 10 years ago - 1 comment

#14 - support inversions with leading base

Issue - State: closed - Opened by jn80842 over 10 years ago - 1 comment

#13 - SMaSH crashes on VCFs with no genotyping information at all

Issue - State: closed - Opened by jn80842 over 10 years ago - 1 comment

#12 - annotated VCF output from bench.py is not sorted by position

Issue - State: closed - Opened by jn80842 over 10 years ago - 1 comment

#11 - Update README.md

Pull Request - State: closed - Opened by godotgildor over 10 years ago - 1 comment

#10 - Variant with N ref/alt alleles causes normalization to throw an exception

Issue - State: closed - Opened by jn80842 over 10 years ago - 1 comment

#8 - SMaSH does not evaluate compound het variants correctly

Issue - State: open - Opened by jn80842 over 10 years ago

#7 - normalized variant can be placed at same position as existing variant

Issue - State: closed - Opened by jn80842 over 10 years ago - 1 comment

#6 - Here is the system test we discussed

Pull Request - State: closed - Opened by kwestbrooks over 10 years ago

#5 - Option to write out "rescued" version of second input vcf

Issue - State: closed - Opened by jn80842 over 10 years ago - 1 comment
Labels: enhancement

#4 - Factor out unnecessary asserts

Issue - State: open - Opened by jn80842 over 10 years ago

#3 - Preserve genotype information when outputting vcf files

Issue - State: closed - Opened by jn80842 over 10 years ago - 1 comment

#2 - Add documentation source code to repository

Issue - State: open - Opened by spaugh over 10 years ago

#1 - Push SMaSH towards easier programmatic use

Pull Request - State: closed - Opened by spaugh almost 11 years ago - 6 comments