Related Issues (20)
- Subsampling option
- State & transition merging
- Cancer signature models
- --aggregate option to collect all similarly-labeled transitions
- --eliminate-fast option to eliminate redundant states
- Replace --weight-input and --weight-output with macros
- Donβt build namespace if one machine has all-bull state ids
- Graph-grammar decoding HOT 1
- Poly-A tail length caller
- Implement intersection for I/O transducers
- Counts returns half of expected value HOT 1
- Specialized code generators HOT 1
- Options to make a model local by adding flanking states
- Linear-space Forward implementation
- Machine Boss --prefix-backtrack does not seem to work
- Zero-length FASTA sequences crash kseq
- Regular expression parser
- Expression grammar
- Transliteration grammar HOT 1
- Implement HMMER's handling of X's (for protein) and N's (for DNA)
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