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Prep for merge with main and 0.5.0 release
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Improvements to numerical stability of Binomial model (scaling)
Improvements to quality-of-life
  * Compute and propagate seqcol signature of reference used for
  alignment
  * Let orientation flag override filter groups
  * Introuce basic +/-/. for orientation filters
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Rob Patro committed Jul 29, 2024
1 parent 48a0318 commit d80eefe
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Showing 2 changed files with 3 additions and 3 deletions.
4 changes: 2 additions & 2 deletions Cargo.toml
Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,7 @@ categories = ["command-line-utilities", "science"]
seqcol_rs = { git = "https://github.com/COMBINE-lab/seqcol_rs", branch = "dev", version = "0.1.0" }
anyhow = "1.0.86"
bio-types = { version = "1.0.3", features = ["serde"] }
clap = { version = "4.5.10", features = ["derive"] }
clap = { version = "4.5.11", features = ["derive"] }
coitrees = "0.4.0"
noodles-bam = "0.65.0"
noodles-gtf = "0.30.0"
Expand All @@ -49,7 +49,7 @@ csv = "1.3"
ndarray = "0.15"
serde = { version = "1", features = ["derive"] }
itertools = "0.13.0"
serde_json = "1.0.120"
serde_json = "1.0.121"
path-tools = "0.1.0"
atomic_float = "1.0.0"
rand = "0.8.5"
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2 changes: 1 addition & 1 deletion src/main.rs
Original file line number Diff line number Diff line change
Expand Up @@ -189,7 +189,7 @@ fn get_filter_opts(args: &Args) -> AlignmentFilters {
/// will be written to the corresponding `meta_info.json` file for this run.
fn get_json_info(args: &Args, emi: &EMInfo, seqcol_digest: &str) -> serde_json::Value {
let prob = if args.model_coverage {
"binomial"
"scaled_binomial"
} else {
"no_coverage"
};
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