mlin/spvcf issues and pull requests

#31 - Transcoder class should have a virtual destructor

Issue - State: open - Opened by RussellTaylor about 1 year ago

#30 - --with-missing-fields: fill missing AD with {DP},0

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

#29 - --with-missing-fields: pad AD & PL to expected vector length

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

#28 - add --with-missing-fields decoder option

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

#27 - update to htslib 1.17 and libdeflate 1.18

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

#26 - Fields lost from squeezed output if DP not present in input

Issue - State: closed - Opened by RussellTaylor about 3 years ago - 3 comments

#25 - filtering spvcf

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

#24 - convey PL ~ DP regression model

Issue - State: open - Opened by mlin over 4 years ago
Labels: enhancement

#23 - sample subset extraction in spvcf decode

Issue - State: open - Opened by mlin over 4 years ago
Labels: enhancement

#22 - optionally preserve binned GQ

Issue - State: open - Opened by mlin over 4 years ago
Labels: enhancement

#21 - configurable resolution for DP squeezing

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

#21 - configurable resolution for DP squeezing

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

#20 - configurable resolution for squeezed DP

Issue - State: closed - Opened by mlin almost 6 years ago - 1 comment

#19 - polishing release candidate

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

#19 - polishing release candidate

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

#18 - tabix: fast mode to get variant cells only

Issue - State: open - Opened by mlin almost 6 years ago
Labels: enhancement

#17 - Change --squeeze from opt-in to opt-out

Issue - State: closed - Opened by mlin almost 6 years ago

#17 - Change --squeeze from opt-in to opt-out

Issue - State: closed - Opened by mlin almost 6 years ago

#16 - align checkpoints with BGZF block boundaries

Issue - State: open - Opened by mlin almost 6 years ago
Labels: bug

#15 - change ##fileformat= header to and fro

Issue - State: closed - Opened by mlin about 6 years ago

#15 - change ##fileformat= header to and fro

Issue - State: closed - Opened by mlin about 6 years ago

#14 - better input validation

Issue - State: closed - Opened by mlin over 6 years ago - 1 comment

#14 - better input validation

Issue - State: closed - Opened by mlin over 6 years ago - 1 comment

#13 - Multithreaded encoder

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

#13 - Multithreaded encoder

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

#12 - Add SPEC.md

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

#12 - Add SPEC.md

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

#11 - Format spec

Issue - State: closed - Opened by mlin over 6 years ago

#11 - Format spec

Issue - State: closed - Opened by mlin over 6 years ago

#10 - tabix slicing improvements

Issue - State: open - Opened by mlin over 6 years ago - 1 comment
Labels: bug

#9 - tabix slicing

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

#9 - tabix slicing

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

#8 - General questions

Issue - State: closed - Opened by fritzsedlazeck over 6 years ago - 3 comments

#8 - General questions

Issue - State: closed - Opened by fritzsedlazeck over 6 years ago - 3 comments

#7 - Multithreaded encoder

Issue - State: closed - Opened by mlin over 6 years ago

#7 - Multithreaded encoder

Issue - State: closed - Opened by mlin over 6 years ago

#6 - tabix slicing

Issue - State: closed - Opened by mlin over 6 years ago - 1 comment

#6 - tabix slicing

Issue - State: closed - Opened by mlin over 6 years ago - 1 comment

#5 - speed up encoder

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

#5 - speed up encoder

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

#4 - Smart squeezing

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

#4 - Smart squeezing

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

#3 - Checkpointing

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

#3 - Checkpointing

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

#2 - Lossy "squeeze" mode: discard QC measures for cells with no ALT called

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

#2 - Lossy "squeeze" mode: discard QC measures for cells with no ALT called

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

#1 - initial readme

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

#1 - initial readme

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

GitHub / mlin/spvcf issues and pull requests