hoffmangroup segway issues

hoffmangroup / segway

Application for semi-automated genomic annotation.

http://segway.hoffmanlab.org/

GNU General Public License v2.0

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issues

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Cannot create observations before training and annotation

#132 EricR86 opened 5 years ago
0
Touchstone exists for simplereverse but is never checked

#131 EricR86 opened 5 years ago
0
Simpleseg jobs.instance.tab ocassionally has out of order output

#130 EricR86 opened 5 years ago
1
Segway with EGBR

#129 EricR86 opened 6 years ago
0
Stale file handle error

#128 EricR86 opened 6 years ago
3
Give users controls over track weights.

#127 EricR86 opened 6 years ago
2
Segway uses ez_setup and puts it on the PYTHONPATH

#126 EricR86 closed 1 year ago
0
--dry-run fatal TypeError

#125 EricR86 closed 6 years ago
4
Warn users when the number of windows exceed a threshold

#124 EricR86 opened 6 years ago
5
Setting hard memory limit constraints fails on certain systems

#123 EricR86 opened 6 years ago
0
save_gmtk_input() hides exception raised by genomedata

#122 EricR86 opened 6 years ago
1
--include-coord does not verify if the coordinates are valid before running Segway

#121 EricR86 opened 6 years ago
2
Fatal fdiffact1 error when using --semisupervised and --validation-coords together

#120 EricR86 opened 6 years ago
1
--semisupervised mode fails when no tracks are specified

#119 EricR86 opened 6 years ago
0
Test segway_layer_bigbed fails due to difference in bigBed files

#118 EricR86 opened 7 years ago
0
Windows with multiple Genomedata archives are erroneously chosen with missing data

#117 EricR86 closed 6 years ago
5
Add feature to not annotate features where there is no data for regions over a certain bp/ruler threshold

#116 EricR86 opened 7 years ago
0
Reverse world option creates a single annotation

#115 EricR86 closed 7 years ago
5
Standard output not being captured

#114 EricR86 closed 6 years ago
4
Accounting for Gaussian components vanishing upon reaching 0 probability mass

#113 EricR86 closed 5 years ago
8
Segway should use subcommand parsers to distinguish options between verbs

#112 EricR86 opened 7 years ago
0
Issues not being sent to segway-internal mailing list, test 3

#111 EricR86 opened 7 years ago
0
Issues not being sent to segway-internal mailing list

#110 EricR86 closed 7 years ago
1
Segway should have an error or warn if there's an option specified that is not found

#109 EricR86 opened 7 years ago
0
Test issue, please ignore

#108 EricR86 closed 7 years ago
1
Refactor out repetition between generate_objects methods in ParamSpec classes

#107 EricR86 opened 7 years ago
1
Segway should output a better error message for empty tracks

#106 EricR86 opened 7 years ago
1
Add --no-version-check to Segway options

#105 EricR86 opened 7 years ago
0
Segway/GMTK errors out when a track contains all equal values

#104 EricR86 opened 7 years ago
0
Error for training

#103 EricR86 closed 7 years ago
1
Testing should be seperated between segway-task and segway as a dry run

#102 EricR86 opened 7 years ago
0
Tags on bitbucket pipelines should automatically perform a release

#101 EricR86 opened 7 years ago
5
--dinucleotide option and "use_dinucleotide" doesn't seem to work

#100 EricR86 opened 7 years ago
0
Likelihood validation when using minibatch

#99 EricR86 opened 7 years ago
2
New verb for Segway to test likelihood

#98 EricR86 opened 7 years ago
3
--observations option continues looking in traindir even after observations folder is separately specified

#97 EricR86 opened 7 years ago
1
Allow GMTK to use NAN for observations

#96 EricR86 opened 8 years ago
1
Runtime error. Error 126 in output files. Permission denied over sh executable files

#95 EricR86 closed 8 years ago
1
Command to clean up intermediate files from Segway runs

#94 EricR86 opened 8 years ago
3
Jobs.tab occassionally missing lines - line Buffering for jobs.tab

#93 EricR86 opened 8 years ago
11
Segway reporting impossible CPU times?

#92 EricR86 opened 8 years ago
2
Lack of multiple worlds test

#91 EricR86 opened 8 years ago
1
Viterbi in segway-task captures all output and hides warnings

#90 EricR86 opened 8 years ago
0
segway-task should ensure PyTables runs with a single thread

#89 EricR86 opened 8 years ago
0
seg_subseg objects should not be used when hierarchical segmentation is not enabled

#88 EricR86 opened 8 years ago
3
Enable warnings from GMTK

#87 EricR86 opened 8 years ago
1
Segway Identify crashes on PBS/Torque cluster

#86 EricR86 opened 8 years ago
1
Better random number generation per instance

#85 EricR86 opened 8 years ago
0
GMTK gives zero clique error when supervision labels are directly adjacent

#84 EricR86 opened 8 years ago
4
Segway layered bed file output is not sorted and breaks --bigBed option

#83 EricR86 closed 8 years ago
2

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