koadman proxigenomics issues

koadman / proxigenomics

Hi-C analysis of heterogeneous samples

GNU General Public License v2.0

5 stars 2 forks source link

issues

Newest

Newest Most commented Recently updated Oldest Least commented Least recently updated

Many scripts use "dumb" relative paths.

#50 cerebis opened 8 years ago
0
external binaries using path relative to invocation directory

#49 cerebis opened 8 years ago
1
design primers for carrier DNA

#48 koadman closed 8 years ago
1
Simulation pipeline requires an overarching point of entry

#47 cerebis opened 9 years ago
1
Specify an overall output path

#46 cerebis closed 9 years ago
1
External dependencies and overall structure a mess.

#45 cerebis opened 9 years ago
0
Permutation control split over both file existence and parameter settings

#44 cerebis opened 9 years ago
0
bam2edges and edges2metis should be combined.

#43 cerebis opened 9 years ago
0
reduce redundancy in job scripts

#42 koadman closed 8 years ago
2
Scons/Nestly error

#41 koadman closed 8 years ago
2
Ideally, our generated internal files should have annotation fields.

#40 cerebis opened 9 years ago
1
bcubed.py does not notice when supplied the wrong file format.

#39 cerebis opened 9 years ago
0
add support for running pipeline outside $HOME

#38 koadman opened 9 years ago
0
binaries required by mktree.sh are unavailable

#37 koadman opened 9 years ago
2
Support both Hi-C and meta3C read simulation

#36 cerebis opened 9 years ago
0
Large files and method of parsing BAM

#35 cerebis opened 9 years ago
2
contact_map.py memory usage

#34 koadman opened 9 years ago
10
weighted extended bcubed precision and recall

#33 cerebis opened 9 years ago
3
code review pull request

#32 koadman opened 9 years ago
1
Filesystem latency can cause rollbacks

#31 cerebis closed 9 years ago
1
Update WGS and HiC stages to source reference genome data from evolution step

#30 cerebis closed 9 years ago
0
Place basis sequences and trees somewhere sensible.

#29 cerebis closed 9 years ago
0
Externalize binaries path

#28 cerebis closed 9 years ago
0
Improve exit status propagation and rollback

#27 cerebis closed 9 years ago
0
Some alignment work is redundant.

#26 cerebis closed 9 years ago
0
Add assembly QA to pipeline.

#25 cerebis closed 8 years ago
1
Glob on reference folder requires filter for files

#24 cerebis closed 9 years ago
2
Share related parameters between make files

#23 cerebis closed 9 years ago
0
simforward.py CLI help doesn't show reference and output paths.

#22 cerebis closed 8 years ago
0
Place HPC logs into a log folder

#21 cerebis closed 9 years ago
0
Pipeline path references require refactoring

#20 cerebis opened 9 years ago
0
Figure showing simulation workflow

#19 koadman closed 9 years ago
0
Make pipeline runtime environment agnostic.

#18 cerebis opened 9 years ago
2
Integrate SG evolver

#17 cerebis closed 9 years ago
3
Generated Fastq don't follow a naming convention

#16 cerebis closed 9 years ago
1
Create SNP/mutational associations

#15 cerebis closed 9 years ago
0
Symmetric measures can be used as consensus tests

#14 cerebis opened 10 years ago
0
Soft-clustering descriptive values

#13 cerebis opened 10 years ago
0
Some code is running on the head node

#12 cerebis opened 10 years ago
0
Fix branching of pipeline developmental

#11 cerebis closed 10 years ago
1
Soft-clustering

#10 cerebis opened 10 years ago
1
Ground truth is only a guess

#9 cerebis opened 10 years ago
0
Should performance metrics consider only classification

#8 cerebis opened 10 years ago
0
Edge weighting

#7 cerebis opened 10 years ago
0
Pruning of input graph

#6 cerebis opened 10 years ago
0
The end-to-end workflow needs to be split into parts.

#5 cerebis closed 10 years ago
3
User set random seed

#4 cerebis closed 10 years ago
1
Write out community profile for simulation

#3 cerebis closed 9 years ago
1
Community profile by specifying distribution function

#2 cerebis opened 10 years ago
1
Uniform community flag

#1 cerebis opened 10 years ago
1