fulcrumgenomics/fqtk issues and pull requests

#43 - Adds test for better fgoxide header error and bump fgoxide version.

Pull Request - State: open - Opened by theJasonFan 2 months ago

#42 - doc: Clarify that multiple output types may be specified

Pull Request - State: closed - Opened by msto 2 months ago - 1 comment

#41 - how to obtain demultixepled paired-end reads with same structure as input reads, including cell barcodes / UMIs

Issue - State: closed - Opened by andreiprodan 2 months ago - 2 comments
Labels: question

#40 - Barcodes only in Read 1

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

#39 - Clippy the tests and make it happy.

Pull Request - State: closed - Opened by theJasonFan 4 months ago

#38 - DRAFT: SortFastq

Pull Request - State: open - Opened by kockan 11 months ago

#37 - fq trimming

Pull Request - State: open - Opened by brentp 11 months ago

#36 - Request for example sample-metadata file

Issue - State: open - Opened by JHarrisonEcoEvo 11 months ago - 2 comments

#35 - Add demux to readme.

Pull Request - State: closed - Opened by tfenne 11 months ago

#34 - fqtk demu's usage is full of MarkDown that comes out verbatim on the console

Issue - State: open - Opened by tfenne 11 months ago

#33 - [bugfix] Output type writers were all outputting template reads.

Pull Request - State: closed - Opened by jacarey 12 months ago

#32 - feat: skip too short reads

Pull Request - State: closed - Opened by nh13 about 1 year ago

#31 - Better error when the sample barcode lengths in the meta do not match the barcode lengths in the read structure

Issue - State: open - Opened by nh13 about 1 year ago - 2 comments
Labels: enhancement, good first issue

#30 - feat: allow Ns in the sample barcode

Pull Request - State: closed - Opened by nh13 about 1 year ago

#29 - Support barcodes that have different lengths

Issue - State: open - Opened by nh13 about 1 year ago
Labels: enhancement

#28 - Fails if sample barcodes in the meta.csv are longer than implied by the read structure

Issue - State: open - Opened by nh13 about 1 year ago
Labels: good first issue, help wanted

#27 - FQTK fails if reads are too short

Issue - State: closed - Opened by nh13 over 1 year ago
Labels: good first issue, help wanted

#26 - Do not require comment to have 4 segments

Pull Request - State: closed - Opened by nh13 over 1 year ago

#25 - "Comment in did not have 4 segments" in data from SRA/ENA

Issue - State: closed - Opened by nh13 over 1 year ago
Labels: bug

#24 - Fixing rust version in CI because TOML toolchain was not being honored previously.

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

#23 - Tool-chain version of clippy not being honored

Issue - State: open - Opened by NatPRoach over 1 year ago - 2 comments

#22 - Add 'version' arg to command line derivations

Pull Request - State: closed - Opened by NatPRoach over 1 year ago - 3 comments

#21 - Check skipped sequence?

Issue - State: closed - Opened by mschubert over 1 year ago - 5 comments

#20 - Reserve capacity to avoid multiple re-allocations

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

#19 - Integrate read ahead iterator from fgoxide.

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

#18 - Adding bioconda and crates badges, updating install instructions

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

#17 - Removing publish=false from TOML to prepare for impending crates / bioconda release

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

#16 - Add docs for releasing

Pull Request - State: closed - Opened by nh13 over 1 year ago

#15 - Merge dev into main.

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

#14 - Lots of performance tuning, and then adding adding sequences into read headers.

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

#13 - Adding initial metrics generation.

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

#12 - Adding preallocation vector for ref records

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

#11 - Task 8 - Adding the sample barcodes and molecular barcodes to headers.

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

#10 - Various performance improvements including iterating over ref records, and using mono-pooled writer

Pull Request - State: closed - Opened by NatPRoach over 1 year ago - 2 comments

#9 - bugfix - fixing layered buf reader issue with seq_io

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

#8 - Adding rudimentary caching of barcodes

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

#7 - Adding support for a pooled writer to working core

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

#6 - Implement working core of demux FASTQs without caching and without pooled writing

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

#5 - Implement basic command line for fqtk demux

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

#4 - Task3/sample metadata

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

#3 - New tool: replicate fgbio's SortFastq?

Issue - State: open - Opened by tfenne over 1 year ago
Labels: help wanted

#2 - Task2/basic barcode matching struct

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

#1 - Task1/initial repo setup

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

GitHub / fulcrumgenomics/fqtk issues and pull requests