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GitHub / cerebis/qc3c issues and pull requests

#63 - Error: module 'numpy' has no attribute 'asscalar'

Issue - State: open - Opened by shelkmike over 2 years ago - 2 comments

#62 - Enzyme-free protocol

Issue - State: closed - Opened by gubrins about 3 years ago

#61 - Support for Arima High coverage Hi-C kit

Issue - State: open - Opened by Norbittner over 3 years ago - 10 comments
Labels: enhancement, important

#60 - Provide greater detail when BAM sort order is incorrect.

Issue - State: closed - Opened by cerebis over 3 years ago

#59 - Failure to catch missing header exception

Issue - State: closed - Opened by cerebis over 3 years ago - 2 comments
Labels: bug

#58 - Parsing of BAM header when file is expected to be readname-sorted.

Issue - State: closed - Opened by agilly over 3 years ago - 7 comments

#57 - Add ">20kbp" to the long-range pair counting statistic

Issue - State: open - Opened by cerebis about 4 years ago
Labels: enhancement

#56 - Accommodating mismatches in ligation artefacts.

Issue - State: open - Opened by cerebis about 4 years ago
Labels: enhancement

#55 - Input/Output documentation additiion

Issue - State: closed - Opened by cerebis about 4 years ago
Labels: enhancement

#54 - Increase the maximum separation computed for BAM mode.

Issue - State: open - Opened by cerebis about 4 years ago
Labels: enhancement

#53 - Extended main help to better explain modes

Issue - State: open - Opened by cerebis about 4 years ago
Labels: enhancement

#51 - Handling of split R1/R2 bam files

Issue - State: open - Opened by cerebis about 4 years ago
Labels: enhancement

#50 - Duplicates, flags, tallying and MultiQC report

Issue - State: open - Opened by cerebis about 4 years ago
Labels: enhancement

#49 - Add example data and results and extend docs

Issue - State: open - Opened by cerebis about 4 years ago - 1 comment
Labels: enhancement

#48 - Rename jellyfish conda package

Issue - State: open - Opened by cerebis over 4 years ago

#47 - Old Linux distribution import error "GLIBC_2.23' not found"

Issue - State: open - Opened by cerebis over 4 years ago - 4 comments

#45 - samtools missing from qc3C docker container path

Issue - State: closed - Opened by koadman over 4 years ago - 1 comment

#44 - qc3c missing from path when run via singularity

Issue - State: closed - Opened by koadman over 4 years ago - 1 comment

#43 - qc3C conda failure on CentOS8

Issue - State: open - Opened by koadman over 4 years ago - 4 comments

#41 - Better bootstrap merged to master

Pull Request - State: closed - Opened by cerebis almost 5 years ago

#40 - Conda package import error and problems using Docker image

Issue - State: open - Opened by cerebis almost 5 years ago
Labels: bug

#38 - Mergine multidigest branch into master

Pull Request - State: closed - Opened by cerebis about 5 years ago

#37 - Using longest ligation product can overestimate observed fraction

Issue - State: open - Opened by cerebis about 5 years ago
Labels: enhancement

#36 - Check for input files as soon as possible

Issue - State: open - Opened by cerebis about 5 years ago

#35 - Natural occurrence estimation and correction

Issue - State: closed - Opened by cerebis about 5 years ago - 9 comments
Labels: enhancement

#34 - Add command line meta-options for well known commercial libraries

Issue - State: closed - Opened by cerebis over 5 years ago - 1 comment
Labels: enhancement

#33 - Environments with PYTHONPATH set can mislead docker image.

Issue - State: open - Opened by cerebis almost 6 years ago
Labels: bug

#32 - Handle restriction enzymes with ambiguous sites

Issue - State: closed - Opened by cerebis about 6 years ago - 1 comment

#31 - Counting FastA returns 0

Issue - State: closed - Opened by cerebis about 6 years ago

#30 - Add version and time stamps to JSON report

Issue - State: closed - Opened by cerebis about 6 years ago

#29 - Add pigz to docker images

Issue - State: closed - Opened by cerebis about 6 years ago

#28 - Denominator in long-range fraction

Issue - State: closed - Opened by cerebis about 6 years ago - 1 comment

#27 - Kmer analysis is slow due to Jellyfish SWIG overhead.

Issue - State: open - Opened by cerebis about 6 years ago
Labels: enhancement

#26 - Running singularity container without arguments produces esoteric error message

Issue - State: closed - Opened by cerebis about 6 years ago - 1 comment

#25 - Improve docker useability after more use

Issue - State: closed - Opened by cerebis about 6 years ago - 1 comment

#24 - qc3C depends on samtools

Issue - State: closed - Opened by cerebis about 6 years ago - 1 comment

#23 - qc3C docker and singularity

Issue - State: closed - Opened by cerebis about 6 years ago - 1 comment
Labels: bug, wontfix

#21 - Add docker/singlularity details to documentation

Issue - State: closed - Opened by cerebis about 6 years ago

#20 - could track both full cut-site and vestigal

Issue - State: closed - Opened by cerebis about 6 years ago - 1 comment

#19 - Validate on less commonly used enzymes

Issue - State: closed - Opened by cerebis over 6 years ago - 2 comments

#18 - Fuzzier evidence of junctions

Issue - State: closed - Opened by cerebis over 6 years ago

#17 - In bam mode, report fraction against long references

Issue - State: closed - Opened by cerebis over 6 years ago

#16 - Output report in easily parsed format

Issue - State: closed - Opened by cerebis over 6 years ago - 1 comment

#15 - Improve comment about fraction of reads starting with site

Issue - State: closed - Opened by cerebis over 6 years ago

#14 - update read me for new CLI changes

Issue - State: closed - Opened by cerebis over 6 years ago

#13 - Expected fraction at 50% GC

Issue - State: closed - Opened by cerebis over 6 years ago

#12 - log file should include reproducible details.

Issue - State: closed - Opened by cerebis over 6 years ago - 1 comment

#11 - [AD] singularity build file for jellyfish with python bindings

Pull Request - State: closed - Opened by koadman over 6 years ago

#10 - verify jellyfish import

Issue - State: closed - Opened by cerebis over 6 years ago - 1 comment

#8 - [AD] include all evaluated non-HiC reads in the denominator

Pull Request - State: closed - Opened by koadman over 6 years ago

#7 - Track statistics per read group

Issue - State: closed - Opened by cerebis over 6 years ago

#6 - Create LICENSE

Pull Request - State: closed - Opened by cerebis over 6 years ago

#5 - There is no README.md

Issue - State: closed - Opened by cerebis over 6 years ago

#4 - For cis pairs we could produce additional statistics

Issue - State: closed - Opened by cerebis over 6 years ago

#3 - Consider restructuring the output values as a table

Issue - State: closed - Opened by cerebis over 6 years ago

#2 - Permit naming the output pair log at invocation

Issue - State: closed - Opened by cerebis over 6 years ago - 1 comment
Labels: enhancement

#1 - Track multiple enzymes independently

Issue - State: closed - Opened by cerebis over 6 years ago
Labels: enhancement