hoffmangroup/segway

Issues

• High resolution causes error - Questions about interpretation of results

  #182 opened 8 months ago by ChelseyLin3
  1

• Doc suggestion

  #180 opened 10 months ago by wsnoble
  6

• Clean up unnecessary `__future__` imports

  #174 opened a year ago by michaelmhoffman
  1

• Segway uses ez_setup and puts it on the PYTHONPATH

  #126 opened 2 years ago by EricR86
  0

• Using the '--prior-strength' option causes training to crash

  #136 opened 2 years ago by EricR86
  4

• readthedocs.io documentation regressed on command line output

  #157 opened 2 years ago by EricR86
  0

• emission probability heatmap

  #167 opened 2 years ago by YichaoOU
  5

• parallelization not working?

  #166 opened 2 years ago by YichaoOU
  8

• Training windows is empty

  #164 opened 3 years ago by gaborpapp89
  2

• Recover option for segway annotate

  #159 opened 3 years ago by gaborpapp89
  7

• Using continuous and discrete tracks

  #161 opened 3 years ago by corinsexton
  2

• `--trainable-params` and `-p` equivalent option not available for annotate or posterior

  #156 opened 3 years ago by EricR86
  0

• Large verbosity numbers for "--verbose" breaks exisiting parsing of viterbi output

  #155 opened 3 years ago by EricR86
  0

• Reproducibility of Segway results

  #154 opened 3 years ago by corinsexton
  1

• Extremely long runtime

  #152 opened 3 years ago by corinsexton
  2

• Error while running segway train : "can't tie one track in multiple groups" and "Set of training windows is empty"

  #148 opened 4 years ago by Cheryn-A
  3

• building an image using the dockerfile

  #151 opened 4 years ago by MahShaaban
  2

• Meanings of segment names like 13_Quiescent?

  #150 opened 4 years ago by amadeusX
  2

• Segway produces annotations that are not stictly valid BED files

  #149 opened 4 years ago by EricR86
  1

• Documation of num labels Argument

  #138 opened 4 years ago by EricR86
  2

• Support for IBM Spectrum LSF

  #142 opened 5 years ago by EricR86
  1

• Training windows segway train phase

  #137 opened 5 years ago by EricR86
  0

• Error codes on SLURM

  #134 opened 6 years ago by EricR86
  4

• Missing copy of GPL v2 license

  #135 opened 6 years ago by EricR86
  3

• Accounting for Gaussian components vanishing upon reaching 0 probability mass

  #113 opened 6 years ago by EricR86
  8

• Disabling Gaussian splitting in single-Gaussian case

  #133 opened 6 years ago by EricR86
  0

• Cannot create observations before training and annotation

  #132 opened 6 years ago by EricR86
  0

• Simpleseg jobs.instance.tab ocassionally has out of order output

  #130 opened 6 years ago by EricR86
  1

• Touchstone exists for simplereverse but is never checked

  #131 opened 6 years ago by EricR86
  0

• Segway with EGBR

  #129 opened 7 years ago by EricR86
  0

• --dry-run fatal TypeError

  #125 opened 7 years ago by EricR86
  4

• Stale file handle error

  #128 opened 7 years ago by EricR86
  3

• Give users controls over track weights.

  #127 opened 7 years ago by EricR86
  2

• Standard output not being captured

  #114 opened 7 years ago by EricR86
  4

• Warn users when the number of windows exceed a threshold

  #124 opened 7 years ago by EricR86
  5

• Setting hard memory limit constraints fails on certain systems

  #123 opened 7 years ago by EricR86
  0

• save_gmtk_input() hides exception raised by genomedata

  #122 opened 7 years ago by EricR86
  1

• --include-coord does not verify if the coordinates are valid before running Segway

  #121 opened 7 years ago by EricR86
  2

• Fatal fdiffact1 error when using --semisupervised and --validation-coords together

  #120 opened 7 years ago by EricR86
  1

• --semisupervised mode fails when no tracks are specified

  #119 opened 7 years ago by EricR86
  0

• Windows with multiple Genomedata archives are erroneously chosen with missing data

  #117 opened 7 years ago by EricR86
  5

• Test segway_layer_bigbed fails due to difference in bigBed files

  #118 opened 7 years ago by EricR86
  0

• Add feature to not annotate features where there is no data for regions over a certain bp/ruler threshold

  #116 opened 7 years ago by EricR86
  0

• Reverse world option creates a single annotation

  #115 opened 8 years ago by EricR86
  5

• Segway should use subcommand parsers to distinguish options between verbs

  #112 opened 8 years ago by EricR86
  0

• Issues not being sent to segway-internal mailing list, test 3

  #111 opened 8 years ago by EricR86
  0

• Issues not being sent to segway-internal mailing list

  #110 opened 8 years ago by EricR86
  1

• Test issue, please ignore

  #108 opened 8 years ago by EricR86
  1

• Segway should have an error or warn if there's an option specified that is not found

  #109 opened 8 years ago by EricR86
  0

• Refactor out repetition between generate_objects methods in ParamSpec classes

  #107 opened 8 years ago by EricR86
  1