hoffmangroup / segway

Application for semi-automated genomic annotation.

http://segway.hoffmanlab.org/

hoffmangroup/segway Issues

High resolution causes error - Questions about interpretation of results
Updated 15 days ago1
Doc suggestion
Updated 2 months ago6
Clean up unnecessary `__future__` imports
Closed a year ago1
Segway uses ez_setup and puts it on the PYTHONPATH
Closed a year ago
Using the '--prior-strength' option causes training to crash
Closed a year ago4
readthedocs.io documentation regressed on command line output
Closed a year ago
emission probability heatmap
Updated a year ago5
parallelization not working?
Closed a year ago8
Training windows is empty
Closed 2 years ago2
Recover option for segway annotate
Closed 2 years ago7
Using continuous and discrete tracks
Updated 2 years ago2
`--trainable-params` and `-p` equivalent option not available for annotate or posterior
Updated 3 years ago
Large verbosity numbers for "--verbose" breaks exisiting parsing of viterbi output
Updated 3 years ago
Reproducibility of Segway results
Closed 3 years ago1
Extremely long runtime
Closed 3 years ago2
Error while running segway train : "can't tie one track in multiple groups" and "Set of training windows is empty"
Updated 3 years ago3
building an image using the dockerfile
Closed 3 years ago2
Meanings of segment names like 13_Quiescent?
Updated 3 years ago2
Segway produces annotations that are not stictly valid BED files
Updated 4 years ago1
Documation of num labels Argument
Closed 4 years ago2
Support for IBM Spectrum LSF
Updated 4 years ago1
Training windows segway train phase
Updated 4 years ago
Error codes on SLURM
Closed 5 years ago4
Missing copy of GPL v2 license
Closed 5 years ago3
Accounting for Gaussian components vanishing upon reaching 0 probability mass
Closed 5 years ago8
Disabling Gaussian splitting in single-Gaussian case
Updated 5 years ago
Cannot create observations before training and annotation
Updated 6 years ago
Simpleseg jobs.instance.tab ocassionally has out of order output
Updated 6 years ago1
Touchstone exists for simplereverse but is never checked
Updated 6 years ago
Segway with EGBR
Updated 6 years ago
--dry-run fatal TypeError
Closed 6 years ago4
Stale file handle error
Updated 6 years ago3
Give users controls over track weights.
Updated 6 years ago2
Standard output not being captured
Closed 6 years ago4
Warn users when the number of windows exceed a threshold
Updated 6 years ago5
Setting hard memory limit constraints fails on certain systems
Updated 7 years ago
save_gmtk_input() hides exception raised by genomedata
Updated 7 years ago1
--include-coord does not verify if the coordinates are valid before running Segway
Updated 7 years ago2
Fatal fdiffact1 error when using --semisupervised and --validation-coords together
Updated 7 years ago1
--semisupervised mode fails when no tracks are specified
Updated 7 years ago
Windows with multiple Genomedata archives are erroneously chosen with missing data
Closed 7 years ago5
Test segway_layer_bigbed fails due to difference in bigBed files
Updated 7 years ago
Add feature to not annotate features where there is no data for regions over a certain bp/ruler threshold
Updated 7 years ago
Reverse world option creates a single annotation
Closed 7 years ago5
Segway should use subcommand parsers to distinguish options between verbs
Updated 7 years ago
Issues not being sent to segway-internal mailing list, test 3
Updated 7 years ago
Issues not being sent to segway-internal mailing list
Closed 7 years ago1
Test issue, please ignore
Closed 7 years ago1
Segway should have an error or warn if there's an option specified that is not found
Updated 7 years ago
Refactor out repetition between generate_objects methods in ParamSpec classes
Updated 7 years ago1