hoffmangroup genomedata issues

hoffmangroup / genomedata

The Genomedata format for storing large-scale functional genomics data.

https://genomedata.hoffmanlab.org/

GNU General Public License v2.0

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issues

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Fix consistency in array shape output when track indexing on bigWig files

#69 EricR86 closed 8 months ago
0
Update minimum CPython version to 3.9

#68 EricR86 closed 8 months ago
0
Fix debug representation of chromosomes for bigWig files

#67 EricR86 closed 10 months ago
0
Fix summary statistics for bigWig files to produce 1-dimensional arrays

#66 EricR86 closed 10 months ago
0
Compatibility with Mac

#65 BradBalderson opened 1 year ago
2
Wheel builds should build with the latest HDF5 libraries

#64 EricR86 opened 1 year ago
0
BigWig Integration

#63 EricR86 closed 1 year ago
0
Add CITATION.cff

#62 EricR86 closed 2 years ago
0
HDF5 dependence moved outside of Genome object

#61 EricR86 closed 2 years ago
3
Add mypy to Genomedata CI

#60 EricR86 closed 3 years ago
1
Possible dead code with encoding workaround on C files

#59 EricR86 closed 1 year ago
0
Flake8 lint fix

#58 EricR86 closed 3 years ago
1
Change genomedata-load-data from binary to Python with c-extension

#57 EricR86 closed 3 years ago
6
Chromsome name mapping from assembly reports

#56 EricR86 closed 3 years ago
1
Last line in data/track bed(Graph) file must be a newline

#55 EricR86 opened 3 years ago
0
genomedata-load joins fasta contig name with rest of description line

#54 EricR86 opened 4 years ago
2
Customizible temporary directory

#53 EricR86 closed 4 years ago
1
Newer Genomedata versions should error and warn users during install if 'forked-path' is installed

#52 EricR86 opened 5 years ago
0
Recent genomedata versions break previous (version 1.3.6) masking

#51 EricR86 opened 5 years ago
4
pip install --upgrade genomedata can fail on some systems, due to path.py issues

#50 EricR86 opened 5 years ago
3
Bad error message when genomedata-load-data not found on PATH

#49 EricR86 opened 5 years ago
1
Missing License metadata in pip package

#48 EricR86 opened 5 years ago
1
"assert" statements from genomedata_load_data.c may errenously remove functionality

#47 EricR86 opened 5 years ago
1
Anaconda distribution broken

#46 EricR86 closed 5 years ago
9
`pip install genomedata` attempts to find /usr/bin/gcc-4.0 which may not exist

#45 EricR86 closed 5 years ago
1
Installation problem

#44 EricR86 closed 6 years ago
2
find_chunks in _load_seq.py does not end a chunk early at the end of a supercontig

#43 EricR86 opened 6 years ago
6
Better error messages when files/directories already exist when attempting to create Genomedata archives

#42 EricR86 opened 6 years ago
1
genomedata-load-seq error

#41 EricR86 opened 6 years ago
1
genomedata-erase-data doesn't work

#40 EricR86 opened 6 years ago
5
seqfile_type is None on genomedata-load-seq

#39 EricR86 closed 7 years ago
3
PyTables >= 3.4.1 causes a core dump when reading a continuous section from a supercontig

#38 EricR86 closed 7 years ago
18
_load_data.py python script interface never used

#37 EricR86 opened 7 years ago
2
Genomedata should have a wheel distribution

#36 EricR86 opened 7 years ago
1
The required syntax of load_genomedata is not externally documented

#35 EricR86 opened 7 years ago
1
load_genomedata: responds poorly to invalid syntax [only a pair, `(name, path)`, instead of a list of pairs]

#34 EricR86 opened 7 years ago
1
load_genomedata: responds poorly to invalid syntax [only a track path, instead of (name, path) tuple]

#33 EricR86 opened 7 years ago
6
h5repack segfaults (in rare cases of unknown etiology)

#32 EricR86 closed 4 years ago
6
Genomedata reports a "Segmentation Fault" when running on machines with insufficient memory

#31 EricR86 opened 7 years ago
0
Unsorted input can result in > 100x slower performance

#30 EricR86 opened 7 years ago
5
Docs should include documentation on bigWig support

#29 EricR86 opened 7 years ago
0
Better error message when genomedata-load is not on the PATH

#28 EricR86 opened 7 years ago
0
AttributeError: 'File' object has no attribute 'createGroup' error upon running genomedata-load-seq

#27 EricR86 closed 7 years ago
4
Accessing track-dependent attributes of archives without any tracks results in a fatal error

#26 EricR86 opened 7 years ago
1
Consider changing PyTables default number of threads

#25 EricR86 opened 7 years ago
4
Repeated warning: dataset </supercontig_0/continuous> cannot be read, deflate filter is not available from genomedata-load

#24 EricR86 opened 7 years ago
1
genomedata-load does not throw the correct error when given improper input

#23 EricR86 opened 7 years ago
1
Empty archives when created from an assembly

#22 EricR86 closed 5 years ago
2
genomedata-open-data plural usage of trackname

#21 EricR86 opened 8 years ago
0
Instatallation of Genomedata scripts fails on Python 3

#20 EricR86 closed 1 year ago
0