evoldoers machineboss issues

evoldoers / machineboss

Bioinformatics Open Source Sequence machine

BSD 3-Clause "New" or "Revised" License

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issues

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Implement HMMER's handling of X's (for protein) and N's (for DNA)

#117 ihh opened 4 years ago
0
Transliteration grammar

#116 ihh closed 4 years ago
1
Expression grammar

#115 ihh closed 4 years ago
0
Regular expression parser

#114 ihh closed 4 years ago
0
Zero-length FASTA sequences crash kseq

#113 ihh closed 4 years ago
0
Machine Boss --prefix-backtrack does not seem to work

#112 ihh closed 4 years ago
0
Linear-space Forward implementation

#111 ihh closed 4 years ago
0
Options to make a model local by adding flanking states

#110 ihh closed 4 years ago
0
Specialized code generators

#109 ihh closed 4 years ago
1
Counts returns half of expected value

#108 yuji3w closed 4 years ago
1
Added more floating point handling

#107 yuji3w closed 4 years ago
0
Implement intersection for I/O transducers

#106 ihh opened 5 years ago
0
Poly-A tail length caller

#105 ihh opened 5 years ago
0
Graph-grammar decoding

#104 ihh opened 5 years ago
1
Don’t build namespace if one machine has all-bull state ids

#103 ihh closed 5 years ago
0
Replace --weight-input and --weight-output with macros

#102 ihh closed 5 years ago
0
--eliminate-fast option to eliminate redundant states

#101 ihh closed 5 years ago
0
--aggregate option to collect all similarly-labeled transitions

#100 ihh closed 5 years ago
0
Cancer signature models

#99 ihh opened 5 years ago
0
State & transition merging

#98 ihh opened 5 years ago
0
Subsampling option

#97 ihh closed 5 years ago
0
--local-input, --local-output, and --local

#96 ihh closed 5 years ago
0
No backwards transitions in HMM

#95 ihh closed 5 years ago
1
Optimize advanceSort()

#94 ihh closed 5 years ago
0
Duplicate state names make a machine file unreadable

#93 ihh closed 5 years ago
0
--count-copies creates a cyclic machine (actually an implicit reduction precedence issue)

#92 ihh closed 5 years ago
3
—generate-wild-dna, —generate-wild-aa...

#91 ihh closed 5 years ago
0
Free memory during prefix search

#90 ihh closed 5 years ago
0
COSMIC gene fusion models

#89 ihh opened 5 years ago
0
Jukes-Cantor & TKF91 presets

#88 ihh closed 4 years ago
1
--count-copies argument

#87 ihh closed 5 years ago
0
Parameters defined by "defs" should appear in counts

#86 ihh closed 5 years ago
0
Parameters defined by "defs" should not be eliminated

#85 ihh closed 5 years ago
0
Eliminate prefix options

#84 ihh closed 5 years ago
0
When params are unspecified but there is a norm constraint, assume uniformity

#83 ihh closed 5 years ago
0
Machine.weightInputs and Machine.weightOutputs should add param constraints

#82 ihh closed 5 years ago
0
Count number of copies of a tandem repeat

#81 ihh closed 5 years ago
3
get model by MD5 hash

#80 ihh closed 5 years ago
0
wrapper for codon usage by species

#79 ihh closed 5 years ago
0
machine registry

#78 ihh closed 5 years ago
0
wrappers for REST APIs for Pfam, Uniprot

#77 ihh closed 5 years ago
0
Beam search decoding

#76 ihh closed 5 years ago
0
Try simulated annealing vs prefix search

#75 ihh closed 5 years ago
1
Calculation bugs causing overflows with --output-chars and --decode

#74 ihh closed 5 years ago
0
Generated C++ code crashes clang

#73 ihh closed 5 years ago
0
Estimate transducer entropy

#72 ihh closed 6 years ago
0
Implement CTC prefix search

#71 ihh closed 5 years ago
0
Options for explicit control over advanceSort() & advancingMachine()

#70 ihh closed 6 years ago
0
protpsw->translate->dna2 crashes out when an expression string hits 2Gb

#69 ihh closed 6 years ago
1
Add test for --memoize, including idempotence

#68 ihh opened 6 years ago
0