Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / evoldoers/machineboss issues and pull requests

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

Issue - State: open - Opened by ihh over 4 years ago
Labels: enhancement

#116 - Transliteration grammar

Issue - State: closed - Opened by ihh almost 5 years ago - 1 comment
Labels: enhancement, wontfix

#115 - Expression grammar

Issue - State: closed - Opened by ihh almost 5 years ago
Labels: enhancement

#114 - Regular expression parser

Issue - State: closed - Opened by ihh almost 5 years ago
Labels: enhancement

#113 - Zero-length FASTA sequences crash kseq

Issue - State: closed - Opened by ihh almost 5 years ago
Labels: bug

#112 - Machine Boss --prefix-backtrack does not seem to work

Issue - State: closed - Opened by ihh almost 5 years ago
Labels: bug

#111 - Linear-space Forward implementation

Issue - State: closed - Opened by ihh almost 5 years ago
Labels: enhancement

#110 - Options to make a model local by adding flanking states

Issue - State: closed - Opened by ihh almost 5 years ago
Labels: enhancement

#109 - Specialized code generators

Issue - State: closed - Opened by ihh almost 5 years ago - 1 comment
Labels: enhancement, wontfix, compiler

#108 - Counts returns half of expected value

Issue - State: closed - Opened by yuji3w about 5 years ago - 1 comment

#107 - Added more floating point handling

Pull Request - State: closed - Opened by yuji3w about 5 years ago

#106 - Implement intersection for I/O transducers

Issue - State: open - Opened by ihh almost 6 years ago
Labels: enhancement

#105 - Poly-A tail length caller

Issue - State: open - Opened by ihh almost 6 years ago
Labels: nanopore, application

#104 - Graph-grammar decoding

Issue - State: open - Opened by ihh about 6 years ago - 1 comment
Labels: enhancement

#103 - Don’t build namespace if one machine has all-bull state ids

Issue - State: closed - Opened by ihh about 6 years ago

#102 - Replace --weight-input and --weight-output with macros

Issue - State: closed - Opened by ihh about 6 years ago
Labels: enhancement, nanopore

#101 - --eliminate-fast option to eliminate redundant states

Issue - State: closed - Opened by ihh about 6 years ago
Labels: enhancement, nanopore

#100 - --aggregate option to collect all similarly-labeled transitions

Issue - State: closed - Opened by ihh about 6 years ago
Labels: enhancement, wontfix, nanopore

#99 - Cancer signature models

Issue - State: open - Opened by ihh about 6 years ago
Labels: enhancement, application

#98 - State & transition merging

Issue - State: open - Opened by ihh about 6 years ago
Labels: enhancement, nanopore

#97 - Subsampling option

Issue - State: closed - Opened by ihh about 6 years ago
Labels: enhancement, nanopore

#96 - --local-input, --local-output, and --local

Issue - State: closed - Opened by ihh about 6 years ago

#95 - No backwards transitions in HMM

Issue - State: closed - Opened by ihh about 6 years ago - 1 comment
Labels: wontfix

#94 - Optimize advanceSort()

Issue - State: closed - Opened by ihh about 6 years ago

#93 - Duplicate state names make a machine file unreadable

Issue - State: closed - Opened by ihh about 6 years ago
Labels: bug

#92 - --count-copies creates a cyclic machine (actually an implicit reduction precedence issue)

Issue - State: closed - Opened by ihh about 6 years ago - 3 comments
Labels: bug

#91 - —generate-wild-dna, —generate-wild-aa...

Issue - State: closed - Opened by ihh about 6 years ago

#90 - Free memory during prefix search

Issue - State: closed - Opened by ihh about 6 years ago

#89 - COSMIC gene fusion models

Issue - State: open - Opened by ihh about 6 years ago
Labels: nanopore, application

#88 - Jukes-Cantor & TKF91 presets

Issue - State: closed - Opened by ihh about 6 years ago - 1 comment
Labels: enhancement

#87 - --count-copies argument

Issue - State: closed - Opened by ihh about 6 years ago

#86 - Parameters defined by "defs" should appear in counts

Issue - State: closed - Opened by ihh about 6 years ago

#85 - Parameters defined by "defs" should not be eliminated

Issue - State: closed - Opened by ihh about 6 years ago
Labels: bug

#84 - Eliminate prefix options

Issue - State: closed - Opened by ihh about 6 years ago

#81 - Count number of copies of a tandem repeat

Issue - State: closed - Opened by ihh about 6 years ago - 3 comments
Labels: application

#80 - get model by MD5 hash

Issue - State: closed - Opened by ihh about 6 years ago

#79 - wrapper for codon usage by species

Issue - State: closed - Opened by ihh about 6 years ago

#78 - machine registry

Issue - State: closed - Opened by ihh about 6 years ago

#77 - wrappers for REST APIs for Pfam, Uniprot

Issue - State: closed - Opened by ihh about 6 years ago
Labels: enhancement

#76 - Beam search decoding

Issue - State: closed - Opened by ihh about 6 years ago
Labels: enhancement

#75 - Try simulated annealing vs prefix search

Issue - State: closed - Opened by ihh about 6 years ago - 1 comment
Labels: enhancement

#74 - Calculation bugs causing overflows with --output-chars and --decode

Issue - State: closed - Opened by ihh about 6 years ago
Labels: bug

#73 - Generated C++ code crashes clang

Issue - State: closed - Opened by ihh about 6 years ago
Labels: bug

#72 - Estimate transducer entropy

Issue - State: closed - Opened by ihh over 6 years ago

#71 - Implement CTC prefix search

Issue - State: closed - Opened by ihh over 6 years ago
Labels: enhancement

#69 - protpsw->translate->dna2 crashes out when an expression string hits 2Gb

Issue - State: closed - Opened by ihh over 6 years ago - 1 comment
Labels: bug, wontfix

#68 - Add test for --memoize, including idempotence

Issue - State: open - Opened by ihh over 6 years ago
Labels: bug, test

#67 - Node script to generate context-sensitive error model

Issue - State: closed - Opened by ihh over 6 years ago
Labels: nanopore, application

#66 - Banded initializer for Envelope

Issue - State: open - Opened by ihh over 6 years ago
Labels: enhancement

#65 - --accept-wild and --generate-wild

Issue - State: closed - Opened by ihh over 6 years ago
Labels: enhancement

#64 - Rename presets consistently

Issue - State: open - Opened by ihh over 6 years ago

#63 - ham output

Issue - State: open - Opened by ihh over 6 years ago
Labels: enhancement, compiler

#62 - HMMoC output

Issue - State: open - Opened by ihh over 6 years ago
Labels: enhancement, compiler

#61 - StochHMM output

Issue - State: open - Opened by ihh over 6 years ago
Labels: enhancement, compiler

#60 - BCR annotation from V(D)J-aware HMM

Issue - State: open - Opened by ihh over 6 years ago
Labels: application

#59 - Parse ham yaml files

Issue - State: open - Opened by ihh over 6 years ago - 1 comment
Labels: enhancement

#58 - Add --data-stockholm option to specify training data as file of pairwise alignments

Issue - State: open - Opened by ihh over 6 years ago - 1 comment
Labels: enhancement

#57 - Protein-to-basecalled-read with nanopore-trained error model

Issue - State: open - Opened by ihh over 6 years ago
Labels: nanopore, application

#56 - Transmembrane protein prediction from DNA

Issue - State: open - Opened by ihh over 6 years ago
Labels: application

#55 - --generate-chars and --input-chars, etc

Issue - State: closed - Opened by ihh over 6 years ago
Labels: enhancement

#54 - Add --generate-fasta and --accept-fasta options

Issue - State: closed - Opened by ihh over 6 years ago
Labels: enhancement

#53 - CUDA code generation

Issue - State: open - Opened by ihh over 6 years ago
Labels: compiler

#52 - Viterbi code generation

Issue - State: closed - Opened by ihh over 6 years ago
Labels: compiler

#51 - JSON machine expression schema

Issue - State: closed - Opened by ihh over 6 years ago
Labels: enhancement

#50 - Bitstutter indel test

Issue - State: open - Opened by ihh over 6 years ago
Labels: compiler, test

#49 - JavaScript compiler test

Issue - State: closed - Opened by ihh over 6 years ago
Labels: compiler, test

#48 - Sequence likelihood test

Issue - State: closed - Opened by ihh over 6 years ago
Labels: nanopore, test

#47 - DNA sequence to RNN test

Issue - State: closed - Opened by ihh over 6 years ago - 1 comment
Labels: compiler, test

#46 - Bitnoise tests

Issue - State: closed - Opened by ihh over 6 years ago
Labels: compiler, test

#45 - Integer scores

Issue - State: closed - Opened by ihh over 6 years ago
Labels: enhancement, compiler

#44 - Protein to DNA test (compiled)

Issue - State: open - Opened by ihh over 6 years ago
Labels: compiler, test

#43 - Protein to DNA tests

Issue - State: open - Opened by ihh over 6 years ago
Labels: test

#42 - Simulator

Issue - State: open - Opened by ihh over 6 years ago - 1 comment
Labels: enhancement

#41 - Protein HMM to DNA test (compiled)

Issue - State: open - Opened by ihh over 6 years ago
Labels: compiler, test

#40 - Implement Viterbi algorithm in JavaScript

Issue - State: closed - Opened by ihh over 6 years ago - 2 comments
Labels: duplicate, enhancement

#39 - Make Compiler output standalone

Issue - State: closed - Opened by ihh over 6 years ago - 1 comment
Labels: enhancement, compiler

#38 - Optionally allow sequences instead of profiles in Compiler

Issue - State: closed - Opened by ihh over 6 years ago
Labels: enhancement, nanopore, compiler

#37 - Toposort parameters by dependencies, check for cycles

Issue - State: closed - Opened by ihh over 6 years ago
Labels: bug

#36 - Machine should have ParamDefs

Issue - State: closed - Opened by ihh over 6 years ago - 1 comment

#35 - Machine.writeJson should show params

Issue - State: closed - Opened by ihh over 6 years ago

#34 - Machine should have Constraints

Issue - State: closed - Opened by ihh over 6 years ago - 1 comment

#33 - Protein HMM to RNN test

Issue - State: open - Opened by ihh over 6 years ago
Labels: nanopore, compiler, test

#32 - Protein HMM to DNA test

Issue - State: open - Opened by ihh over 6 years ago - 2 comments
Labels: test

#31 - Optimize JSON model serialization by memoizing functions

Issue - State: closed - Opened by ihh over 6 years ago

#30 - Pairwise dynamic programming to CSV profiles

Issue - State: closed - Opened by ihh over 6 years ago - 2 comments
Labels: nanopore

#29 - Fix "Eliminating backward silent transitions" progress

Issue - State: closed - Opened by ihh over 6 years ago
Labels: bug

#28 - Change caller from mixture-of-geometrics to negative binomial

Issue - State: closed - Opened by ihh over 7 years ago - 1 comment
Labels: enhancement, nanopore

#27 - Optionally allow nanomachine to use fast5 segmenting

Issue - State: closed - Opened by ihh over 7 years ago
Labels: enhancement, nanopore

#26 - Use method of moments for quick-fit of scale & shift

Issue - State: closed - Opened by ihh over 7 years ago
Labels: enhancement, wontfix, nanopore

#25 - segmenter not working

Issue - State: closed - Opened by ihh over 7 years ago
Labels: bug, nanopore

#24 - Option to load TraceParams from file

Issue - State: closed - Opened by ihh over 7 years ago
Labels: enhancement, nanopore

#23 - Tighter priors on scale & shift

Issue - State: closed - Opened by ihh over 7 years ago
Labels: enhancement, wontfix, nanopore

#22 - ViterbiMatrix should not softplus all transitions

Issue - State: closed - Opened by ihh over 7 years ago
Labels: bug, enhancement, wontfix, nanopore

#21 - forward & backward likelihoods don't match on seq1-test1.raw

Issue - State: closed - Opened by ihh over 7 years ago
Labels: bug, nanopore

#18 - Alignment-constrained Baum-Welch

Issue - State: closed - Opened by ihh over 7 years ago - 1 comment
Labels: duplicate, enhancement

#17 - Alignment envelopes

Issue - State: closed - Opened by ihh over 7 years ago
Labels: enhancement

#5 - JavaScript Viterbi code generation

Issue - State: closed - Opened by ihh over 7 years ago - 2 comments