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Correct repair matching, ordering, and atomic output #711

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Correct repair matching, ordering, and atomic output #711

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619efb1
Add generic ordered scheduler for repair
SuhasSrinivasan Aug 10, 2026
69db1a2
Preserve repair query-name and output ordering
SuhasSrinivasan Aug 10, 2026
d0b47e2
Make repair output atomic on fatal errors
SuhasSrinivasan Aug 10, 2026
23709cf
Reject overlapping repair placements
SuhasSrinivasan Aug 11, 2026
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2 changes: 1 addition & 1 deletion modkit-core/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -49,6 +49,7 @@ rustc-hash = "1.1.0"
rv = "=0.16.0"
statrs = "0.16.0"
substring = "1.4.5"
tempfile = "3.2"
thiserror = "2.0.11"
tokio = "1.42.0"
tracing = "0.1.41"
Expand All @@ -59,5 +60,4 @@ serde_json = "1.0.149"
[dev-dependencies]
assert_approx_eq = "1.1.0"
similar-asserts = "1.4.2"
tempfile = "3.2"
serde = {version = "1.0.219", features = ["derive"]}
1 change: 1 addition & 0 deletions modkit-core/src/lib.rs
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Expand Up @@ -16,6 +16,7 @@ pub mod mod_base_code;
pub mod modbam_util;
pub mod monoid;
pub mod motifs;
pub(crate) mod ordered_scheduler;
pub mod pileup;
pub mod position_filter;
pub mod read_ids_to_base_mod_probs;
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