dorbarker/voc-identify issues and pull requests

#43 - Output fails when using YAML files

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

#42 - add --input as synonym of --bam

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

#41 - cooccurrence_matrices/absolute lists wrong SNP

Issue - State: open - Opened by ibseq about 3 years ago - 7 comments

#40 - Add support for SAM and CRAM files

Issue - State: open - Opened by dorbarker over 3 years ago - 1 comment
Labels: enhancement

#39 - fix name of pyyaml package

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

#38 - PHE mutations

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

#37 - Read PHE variant definitions directly

Issue - State: closed - Opened by dorbarker over 3 years ago
Labels: enhancement

#36 - More informative error on failed mutations file parse

Issue - State: closed - Opened by dorbarker over 3 years ago
Labels: enhancement

#35 - Dedup

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

#34 - Optionally save internal representation of results

Issue - State: open - Opened by dorbarker over 3 years ago
Labels: enhancement

#33 - running multiple bam files

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

#32 - issue runnign snakemake workflow voc-identify.smk

Issue - State: closed - Opened by ibseq over 3 years ago - 13 comments

#31 - snakemake

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

#30 - Reorg

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

#29 - Enhanced summary

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

#28 - Enhanced summary

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

#27 - Reorganize project

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

#26 - Fix deletion overlap

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

#25 - Deduplicate reads

Issue - State: closed - Opened by dorbarker over 3 years ago
Labels: enhancement

#24 - Alternate subtitiutions

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

#23 - Cut memory use

Issue - State: closed - Opened by dorbarker over 3 years ago
Labels: enhancement

#22 - Validate substitution and insertion format in mutations file at parse time

Issue - State: closed - Opened by dorbarker over 3 years ago
Labels: enhancement

#21 - Insertions

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

#20 - Fix revcomp handling and refactor parsing

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

#19 - Handling of reverse complementation is probably broken

Issue - State: closed - Opened by dorbarker over 3 years ago
Labels: bug

#18 - convert count of positions in a voc to bitarray

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

#17 - Qol

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

#16 - Fix miscalculation of read overlap for deletions

Issue - State: closed - Opened by dorbarker over 3 years ago

#15 - change alignment DF to Series

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

#14 - Clean up type hints

Issue - State: closed - Opened by dorbarker over 3 years ago

#13 - Add proportion of overlapping reads to read species

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

#12 - Dels and multibase

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

#11 - Dels and multibase

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

#10 - Output fails if VOC name has a forward slash in it

Issue - State: closed - Opened by dorbarker over 3 years ago

#9 - Illumina

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

#8 - Support Illumina reads

Issue - State: closed - Opened by dorbarker over 3 years ago

#7 - fix bug with rev comp reads

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

#6 - --delimiter CLI argument

Issue - State: closed - Opened by dorbarker over 3 years ago

#5 - Add test data

Issue - State: closed - Opened by dorbarker over 3 years ago

#4 - Create LICENSE

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

#3 - Support multi-base substitutions

Issue - State: closed - Opened by dorbarker over 3 years ago

#2 - Support point deletions

Issue - State: closed - Opened by dorbarker over 3 years ago

#1 - Mutation format

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

GitHub / dorbarker/voc-identify issues and pull requests