v0.1.97

Kvg fix docker deps (#44)

• Fix Docker dependencies

• Perform phasing in parallel chunks

v0.1.96

Kvg phase (#43)

• Remove dust and repetitive noise kmers from cleaning graph

• Correct reads using a sliding window approach

• New command (call) to emit two fully phased haplotypes

v0.1.95

Kvg clean read bubbles (#42)

• Correct reads by popping bubbles induced against the cleaned graph

• Only replace poor-scoring read paths

v0.1.94

Kvg improve coassemble (#40)

• Fixed an issue where unmapped reads don't have a tid, thus can't be directly unwrapped

• Discard reads that have any non-A/C/G/T bases.

• Improve alignment trimming for proper variant characterization

• Small improvements to superbubble cleaning

• Improvements to training, simplification

v0.1.93

Reverted rescue.rs to version that doesn't attempt to guess locations of relevant reads

v0.1.92

Fix minor lint warnings and improve code quality (#25)

• optimize imports and remove unused imports
• unused variables commented out or underscore applied
• comment unused functions
• snake based name for anchorseq
• clippy: add #[must_use] to functions
• Fix: Disambiguate to_owned method call in graph.insert to resolve multiple applicable items error
• Fix: Correct function signatures to resolve Clippy lints errors
• Fix: Change argument to be passed by reference instead of by value
• Fix: error: boolean to int conversion using if. for in_degree and out_degreee functions
• Fix: inefficient_to_string. error: calling to_string on &&std::string::String
• Fix: cast_possible_truncation. error: casting usize to u8 may truncate the value
• Fix: cast_possible_truncation. Example error: casting usize to u8 may truncate the value
• added function doc for function which may panic (cargo lint)
• Fix items in documentation is missing backticks (cargo lint)
• Fix "method/function could have a #[must_use] attribute" (cargo lint)
• Fix "Variables can be used directly in the format" (cargo lint)
• Fix "error: needless use of for_each" (cargo lint)
• Fix "avoid wildcard imports" (cargo lint)
• Fix "avoid implicitly cloning" (cargo lint)
• Fix "docs for function returning Result missing # Errors section" (cargo lint)
• Fix "test function passing of variable type" (cargo lint)
• Fix:removed enumerate where needed, unused imports, unused variables (cargo lint)

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Co-authored-by: bshifaw [email protected]

v0.1.91

Kvg dep cache (#39)

• Cache Rust dependencies

v0.1.90

Kvg dep cache (#38)

• Cache Rust dependencies for faster builds

v0.1.89

Align 150-bp windows from long read panel to reference to guess where to look for short reads (#37)

v0.1.88

Add eval-model command and refactor train command (#36)

• Added rock curves to train.rs, added eval_model.rs

• fixing merger discrepancies, made function to create ml dataset, updated train.sh

• have the eval_model.rs use the function to create datasets in the train.rs file

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Co-authored-by: bshifaw [email protected]