Skip to content

Parsers for common alignment formats that have no existing crates supporting them #172

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
Chris7 wants to merge 2 commits into
base: main
Choose a base branch
from
Open

Parsers for common alignment formats that have no existing crates supporting them #172

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
e440e98
alignment parsers
Chris7 Jun 2, 2026
af8a300
Reoraganize
Chris7 Jun 3, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
51 changes: 49 additions & 2 deletions Cargo.lock
View file
Open in desktop

Some generated files are not rendered by default. Learn more about how customized files appear on GitHub.

5 changes: 3 additions & 2 deletions Cargo.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,8 +21,8 @@ name = "gen"
path = "src/main.rs"

[workspace]
members = [".", "gen-core", "gen-models", "gen-graph", "gen-diff", "gen-tui", "gen-sugiyama", "gen-annotations", "gen-capnp-schemas"]
default-members = [".", "gen-core", "gen-models", "gen-graph", "gen-diff", "gen-capnp-schemas", "gen-annotations"]
members = [".", "gen-core", "gen-models", "gen-graph", "gen-diff", "gen-tui", "gen-sugiyama", "gen-annotations", "gen-capnp-schemas", "gen-parsers"]
default-members = [".", "gen-core", "gen-models", "gen-graph", "gen-diff", "gen-capnp-schemas", "gen-annotations", "gen-parsers"]
exclude = ["gen-python", "gen-r/src/rust"]

[features]
Expand All @@ -37,6 +37,7 @@ gen-core = { path = "gen-core", version = "0.1.31" }
gen-diff = { path = "gen-diff", version = "0.1.31" }
gen-models = { path = "gen-models", version = "0.1.31" }
gen-graph = { path = "gen-graph", version = "0.1.31" }
gen-parsers = { path = "gen-parsers", version = "0.1.31" }
gen-tui = { path = "gen-tui", version = "0.1.31" }
gen-annotations = { path = "gen-annotations", version = "0.1.31" }
gen-capnp-schemas = { path = "gen-capnp-schemas", version = "0.1.31" }
Expand Down
5 changes: 5 additions & 0 deletions fixtures/alignments/plain_names.aln
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
CLUSTAL W (2.1) multiple sequence alignment

Base ACGT
Child A-GT
* **
6 changes: 6 additions & 0 deletions fixtures/alignments/simple.aln
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
CLUSTAL W (2.1) multiple sequence alignment

SeqA.chr1 ACGT
SeqB.chr1 A-GT
SeqC.chr1 ACG-
* **
2 changes: 1 addition & 1 deletion gen-models/src/block_group.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -525,7 +525,7 @@ impl BlockGroup {
)
}

fn copy_contents_from(
pub fn copy_contents_from(
&self,
conn: &GraphConnection,
source_block_group: &BlockGroup,
Expand Down
17 changes: 17 additions & 0 deletions gen-parsers/Cargo.toml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,17 @@
[package]
name = "gen-parsers"
description = "Bioinformatic file format parsers for Gen."
version = "0.1.31"
edition = "2024"
repository = "https://github.com/genhub-bio/gen"
homepage = "https://genhub.bio"
license = "Apache-2.0"

[dependencies]
gen-core = { path = "../gen-core", version = "0.1.31" }
gen-graph = { path = "../gen-graph", version = "0.1.31" }
thiserror = "2.0.18"

[dev-dependencies]
petgraph = "0.6.5"
similar-asserts = "1.7.0"
Loading
Loading