EI-CoreBioinformatics/portcullis issues and pull requests

#65 - terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::program_options::invalid_option_value> >' ') for option '--input-file' is invalid

Issue - State: open - Opened by pameyaw over 1 year ago

#64 - I have two files that are not created when the command is restarting (portcullis.junctions.tab , portcullis.junctions.bed )

Issue - State: open - Opened by sashulkaSh almost 2 years ago

#63 - ResolvePackageNotFound: python=3.1

Issue - State: open - Opened by margaretwoodhouse about 2 years ago - 1 comment

#62 - Using Portcullis on large Datasets in connection with Mikado

Issue - State: open - Opened by cc-prolix about 2 years ago

#61 - Compilation error with python 3.10

Issue - State: open - Opened by dpryan79 over 2 years ago

#60 - Portcullis junc detects no junctions if bam index file already present in bam dir

Issue - State: open - Opened by OXB-DC over 2 years ago

#59 - make fails

Issue - State: open - Opened by francicco almost 3 years ago - 2 comments

#58 - terminate called after throwing an instance of 'boost::wrapexcept<portcullis::bam::BamException>'

Issue - State: open - Opened by mezarque over 3 years ago

#57 - JunctionException using portcullis junc

Issue - State: closed - Opened by cc-prolix over 3 years ago - 1 comment

#56 - autogen.sh autoreconf ERROR

Issue - State: open - Opened by francicco over 4 years ago - 1 comment

#55 - UnsatisfiableError: The following specifications were found to be incompatible with the existing python installation in your environment

Issue - State: closed - Opened by chnych over 4 years ago - 8 comments
Labels: bug

#54 - Handling differences between short and long reads

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

#53 - could not open script file as a python file, any help with this error would be greatly appreciated. after brew install, portcullis full used

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

#52 - missed junction

Issue - State: open - Opened by gorliver almost 5 years ago

#51 - more incorrect number of column errors

Issue - State: open - Opened by adamfreedman almost 5 years ago - 7 comments
Labels: bug

#50 - AttributeError: type object 'DataFrame' has no attribute 'from_csv'

Issue - State: open - Opened by lijing28101 almost 5 years ago - 9 comments
Labels: question

#49 - portcullis::FileSystemError*

Issue - State: open - Opened by Xiaofei-git about 5 years ago - 6 comments

#48 - Read counts

Issue - State: open - Opened by KMgoo over 5 years ago

#47 - Exon is not exactly recognized

Issue - State: closed - Opened by KMgoo over 5 years ago - 12 comments
Labels: enhancement, question

#46 - An error during Filtering junctions

Issue - State: closed - Opened by KMgoo over 5 years ago - 12 comments
Labels: bug

#45 - Added library declaration to properly compile from source

Pull Request - State: closed - Opened by ghost over 5 years ago - 1 comment

#44 - High Novel Splicce Junction Rate

Issue - State: closed - Opened by jgockley62 over 5 years ago - 6 comments

#43 - problem w/ python missing dependency in source installation

Issue - State: open - Opened by rdauria over 5 years ago - 3 comments
Labels: bug, question

#42 - error in portcullis bamfilt

Issue - State: closed - Opened by wenbinmei over 5 years ago - 13 comments
Labels: bug, question

#41 - Make portcullis work with long reads: ideas

Issue - State: open - Opened by lucventurini over 5 years ago - 12 comments
Labels: enhancement

#40 - how does portcullis handle antisense reads?

Issue - State: closed - Opened by mparker2 over 5 years ago - 1 comment

#39 - portcullis::JunctionError*

Issue - State: closed - Opened by lstxmu almost 6 years ago - 4 comments

#38 - [BUG] make check fails with conda python

Issue - State: closed - Opened by lucventurini about 6 years ago - 3 comments

#37 - Parsing Command Line: too many positional options have been specified on the command line

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

#36 - [Singularity] Installation fails, even following instructions in the recipe in the Repo

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

#35 - [BUG] Brew installation now broken after the release of Python 3.7

Issue - State: open - Opened by lucventurini over 6 years ago - 1 comment
Labels: bug

#34 - conda conflicts with enum34?

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

#33 - Using Portcullis on RHEL7

Issue - State: closed - Opened by beechwood13 over 6 years ago - 17 comments
Labels: bug

#32 - Streamline boost subset

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

#31 - Broken junctools convert due to changes in the tab format

Issue - State: closed - Opened by lucventurini almost 7 years ago - 2 comments

#30 - Counts of R1 and R2 for each strand

Issue - State: closed - Opened by maplesond almost 7 years ago - 1 comment

#29 - Ensure unique id after junctools set union

Issue - State: open - Opened by maplesond about 7 years ago
Labels: enhancement

#28 - Added sort / reindex and prefix options to junctools set

Issue - State: open - Opened by maplesond about 7 years ago
Labels: enhancement

#27 - Adapt initial positive set to sequencing depth and read length

Issue - State: open - Opened by maplesond about 7 years ago - 1 comment
Labels: enhancement

#26 - Speed up rule based filtering

Issue - State: closed - Opened by maplesond about 7 years ago - 2 comments

#25 - terminate called after throwing an instance of 'boost::exception_detail::clone_impl<portcullis::JunctionException>' what(): std::exception**

Issue - State: closed - Opened by fcamara7 about 7 years ago - 10 comments

#24 - Investigate use of cross validation for selecting cutoff values.

Issue - State: closed - Opened by maplesond over 7 years ago - 1 comment
Labels: question

#23 - Improve performance of rule-based filtering

Issue - State: closed - Opened by maplesond about 8 years ago - 2 comments
Labels: enhancement

#22 - Trouble starting with non-standard python3

Issue - State: closed - Opened by IanSudbery about 8 years ago - 4 comments

#21 - Configure with python3

Issue - State: closed - Opened by colindaven about 8 years ago - 13 comments

#20 - Define primary junctions

Issue - State: open - Opened by lucventurini over 8 years ago
Labels: enhancement

#19 - Use score instead of coverage for the BED/GFF/GTF output

Issue - State: closed - Opened by lucventurini over 8 years ago - 2 comments
Labels: enhancement

#18 - [0.16.0] Portcullis filter dies as it cannot find the junction file

Issue - State: closed - Opened by lucventurini over 8 years ago - 5 comments
Labels: bug

#17 - Personalise GFF source field in the output

Issue - State: closed - Opened by lucventurini almost 9 years ago - 1 comment
Labels: enhancement

#16 - Portcullis filter dies if the output folder does not exist

Issue - State: closed - Opened by lucventurini almost 9 years ago - 2 comments

#15 - Create subfolders for -o options

Issue - State: closed - Opened by lucventurini about 9 years ago - 3 comments
Labels: enhancement

#14 - Link/Copy BAM index as well if present during prep

Issue - State: closed - Opened by lucventurini about 9 years ago - 1 comment

#13 - Incorrect strand assigned to junctions

Issue - State: closed - Opened by lucventurini about 9 years ago - 9 comments
Labels: bug

#12 - Add "assume sorted" option to prep/full

Issue - State: closed - Opened by lucventurini over 9 years ago - 4 comments

#11 - No linking option in portcullis full

Issue - State: closed - Opened by lucventurini over 9 years ago - 2 comments

#10 - Reconsider how analysis of regions flanking a junction work

Issue - State: closed - Opened by maplesond over 9 years ago - 1 comment
Labels: enhancement

#9 - Change interface to filter tool.

Issue - State: closed - Opened by maplesond over 9 years ago - 1 comment

#8 - New metric: # MSRs in junction

Issue - State: closed - Opened by maplesond almost 10 years ago - 1 comment

#7 - Dig more information from the BAM file.

Issue - State: closed - Opened by maplesond almost 10 years ago - 2 comments

#6 - Create documentation

Issue - State: closed - Opened by maplesond almost 10 years ago - 1 comment

#5 - Output BAM containing spliced reads from junc and filter steps

Issue - State: closed - Opened by maplesond almost 10 years ago - 1 comment

#4 - Add relative intron length as a new metric

Issue - State: closed - Opened by maplesond about 10 years ago - 2 comments

#3 - Unit test resources not copied into distributable

Issue - State: closed - Opened by maplesond over 10 years ago - 1 comment
Labels: bug

#2 - Use normal bam indexing rather than bamtools indexing

Issue - State: closed - Opened by maplesond over 10 years ago - 1 comment
Labels: enhancement

#1 - Add dependency on bamtools

Issue - State: closed - Opened by maplesond over 10 years ago

GitHub / EI-CoreBioinformatics/portcullis issues and pull requests