Ecosyste.ms: Issues

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GitHub / databio/gtars issues and pull requests

#46 - cargo build causes error on newest branch dev_bam_bedgraph_bigtools

Issue - State: closed - Opened by ClaudeHu 12 days ago - 3 comments

#45 - IGD Search is returning 0 hits in some test cases

Issue - State: open - Opened by donaldcampbelljr 13 days ago - 2 comments

#44 - attempt txt input update

Pull Request - State: open - Opened by sanghoonio 16 days ago - 12 comments

#43 - Missing start=setting line in the core file generated by uniwig

Issue - State: open - Opened by saanikat 16 days ago - 3 comments

#42 - Double-tokenizing a `RegionSet` will result in no tokens

Issue - State: open - Opened by nleroy917 22 days ago - 1 comment

#41 - Dev bed graph compress counts

Pull Request - State: closed - Opened by donaldcampbelljr 22 days ago

#40 - Add bam support for counting intervals

Pull Request - State: open - Opened by donaldcampbelljr 24 days ago

#39 - Add basic R bindings

Pull Request - State: open - Opened by nleroy917 25 days ago - 1 comment

#38 - Add fragment file region scoring matrix creation

Pull Request - State: open - Opened by nleroy917 26 days ago

#37 - Add converting files to bigWig

Pull Request - State: closed - Opened by donaldcampbelljr 26 days ago - 1 comment

#36 - Dev narrow peak scoring

Pull Request - State: closed - Opened by donaldcampbelljr 29 days ago - 6 comments

#35 - Add pseudobulking code

Pull Request - State: closed - Opened by nleroy917 about 1 month ago

#34 - Count based on narrowPeak score

Issue - State: open - Opened by donaldcampbelljr about 1 month ago
Labels: likely solved

#33 - Rename uniwig

Issue - State: open - Opened by donaldcampbelljr about 1 month ago
Labels: brainstorming

#32 - Bypass filesystem with uniwig using fifos

Issue - State: open - Opened by nsheff about 1 month ago
Labels: brainstorming

#31 - Performance improvements for writing to .wig files

Pull Request - State: closed - Opened by donaldcampbelljr about 1 month ago

#29 - Error from uniwig regarding mismatched chromosomes in BED and .sizes files

Issue - State: closed - Opened by ClaudeHu 3 months ago - 7 comments
Labels: likely solved

#28 - Implement IGD

Issue - State: open - Opened by nleroy917 4 months ago - 3 comments
Labels: new tool

#27 - Hierarchical tokenizers

Pull Request - State: closed - Opened by nleroy917 5 months ago - 1 comment

#27 - Hierarchical tokenizers

Pull Request - State: closed - Opened by nleroy917 5 months ago - 1 comment

#26 - Rename repository to `gtars`

Pull Request - State: closed - Opened by nleroy917 5 months ago

#26 - Rename repository to `gtars`

Pull Request - State: closed - Opened by nleroy917 5 months ago

#25 - Hierarchical universes and a tokenizer config

Issue - State: open - Opened by nleroy917 5 months ago
Labels: enhancement, brainstorming

#25 - Hierarchical universes and a tokenizer config

Issue - State: open - Opened by nleroy917 5 months ago
Labels: enhancement, brainstorming

#24 - Release `v0.0.13` -- Add fragment file tokenizer

Pull Request - State: closed - Opened by nleroy917 6 months ago - 1 comment

#24 - Release `v0.0.13` -- Add fragment file tokenizer

Pull Request - State: closed - Opened by nleroy917 6 months ago - 1 comment

#23 - Implement a basic fragment file tokenizer

Pull Request - State: closed - Opened by nleroy917 6 months ago

#22 - Fix pything bindings tokenization performance issues

Pull Request - State: closed - Opened by nleroy917 6 months ago

#22 - Fix pything bindings tokenization performance issues

Pull Request - State: closed - Opened by nleroy917 6 months ago

#21 - Python bindings memory leak and performance issues

Issue - State: closed - Opened by nleroy917 6 months ago - 1 comment
Labels: bug, enhancement, help wanted, tokenizers

#21 - Python bindings memory leak and performance issues

Issue - State: closed - Opened by nleroy917 6 months ago - 1 comment
Labels: bug, enhancement, help wanted, tokenizers

#20 - PanicException during tokenization

Issue - State: closed - Opened by ClaudeHu 6 months ago - 9 comments
Labels: bug, enhancement, likely solved

#20 - PanicException during tokenization

Issue - State: closed - Opened by ClaudeHu 6 months ago - 9 comments
Labels: bug, enhancement, likely solved

#19 - Tokenize all the things - genomic omni-model

Issue - State: open - Opened by nleroy917 6 months ago
Labels: brainstorming

#19 - Tokenize all the things - genomic omni-model

Issue - State: open - Opened by nleroy917 6 months ago
Labels: brainstorming

#18 - Python bindings wont build for linux `aarch64`

Issue - State: closed - Opened by nleroy917 6 months ago - 9 comments
Labels: bug, help wanted, likely solved

#18 - Python bindings wont build for linux `aarch64`

Issue - State: closed - Opened by nleroy917 6 months ago - 9 comments
Labels: bug, help wanted, likely solved

#17 - Soft tokenizer

Pull Request - State: closed - Opened by nleroy917 6 months ago

#17 - Soft tokenizer

Pull Request - State: closed - Opened by nleroy917 6 months ago

#16 - Release `v0.0.12`

Pull Request - State: closed - Opened by nleroy917 7 months ago - 2 comments

#16 - Release `v0.0.12`

Pull Request - State: closed - Opened by nleroy917 7 months ago - 2 comments

#15 - Convert to workspace

Issue - State: closed - Opened by nleroy917 7 months ago - 1 comment
Labels: enhancement, wontfix

#14 - Implement an `AnnData` tokenizer

Issue - State: open - Opened by nleroy917 7 months ago
Labels: new tool, tokenizers

#13 - Better tokenization API

Pull Request - State: closed - Opened by nleroy917 7 months ago - 1 comment

#13 - Better tokenization API

Pull Request - State: closed - Opened by nleroy917 7 months ago - 1 comment

#12 - Implement a `return_tensors="pt"` function for the Tokenizers

Issue - State: closed - Opened by nleroy917 7 months ago - 1 comment
Labels: wontfix

#12 - Implement a `return_tensors="pt"` function for the Tokenizers

Issue - State: closed - Opened by nleroy917 7 months ago - 1 comment
Labels: wontfix

#11 - Dev uniwig

Pull Request - State: closed - Opened by donaldcampbelljr 8 months ago - 31 comments

#10 - Inconsistent region numbers

Issue - State: open - Opened by gtzheng 9 months ago - 4 comments
Labels: question

#10 - Inconsistent region numbers

Issue - State: open - Opened by gtzheng 9 months ago - 4 comments
Labels: question

#9 - Dev igd

Pull Request - State: closed - Opened by donaldcampbelljr 10 months ago - 2 comments

#8 - add AIList and bindings

Pull Request - State: closed - Opened by edward9065 11 months ago

#8 - add AIList and bindings

Pull Request - State: closed - Opened by edward9065 11 months ago

#7 - Implement a soft tokenizer

Issue - State: open - Opened by nleroy917 11 months ago - 1 comment
Labels: enhancement

#7 - Implement a soft tokenizer

Issue - State: open - Opened by nleroy917 11 months ago - 1 comment
Labels: enhancement

#6 - Merge master changes into dev branch

Pull Request - State: closed - Opened by edward9065 12 months ago

#6 - Merge master changes into dev branch

Pull Request - State: closed - Opened by edward9065 12 months ago

#5 - The `TokenizedRegionSet` needs to have a `to_ids()` function on it

Issue - State: closed - Opened by nleroy917 12 months ago - 2 comments
Labels: enhancement

#5 - The `TokenizedRegionSet` needs to have a `to_ids()` function on it

Issue - State: closed - Opened by nleroy917 12 months ago - 2 comments
Labels: enhancement

#3 - Core utilities

Pull Request - State: closed - Opened by nleroy917 12 months ago - 6 comments

#2 - Implement some core utils

Issue - State: closed - Opened by nleroy917 about 1 year ago - 1 comment
Labels: new tool

#2 - Implement some core utils

Issue - State: closed - Opened by nleroy917 about 1 year ago - 1 comment
Labels: new tool

#1 - Implement `uniwig`

Issue - State: open - Opened by nleroy917 about 1 year ago - 13 comments
Labels: new tool, likely solved