Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / cbg-ethz/shorah issues and pull requests

#87 - is shorah same as lofreq?

Issue - State: open - Opened by ibseq about 2 years ago - 4 comments

#87 - is shorah same as lofreq?

Issue - State: open - Opened by ibseq about 2 years ago - 4 comments

#86 - Switch to poetry/pybind11

Pull Request - State: closed - Opened by spaceben almost 3 years ago

#86 - Switch to poetry/pybind11

Pull Request - State: closed - Opened by spaceben almost 3 years ago

#85 - Smalt command not found

Issue - State: open - Opened by Ruchank1 almost 3 years ago

#85 - Smalt command not found

Issue - State: open - Opened by Ruchank1 almost 3 years ago

#84 - b2w rewrite to Python

Pull Request - State: open - Opened by spaceben about 3 years ago

#84 - b2w rewrite to Python

Pull Request - State: open - Opened by spaceben about 3 years ago

#83 - Error running Amplicon with diversity option

Issue - State: open - Opened by XU-Nuo over 3 years ago - 3 comments

#83 - Error running Amplicon with diversity option

Issue - State: open - Opened by XU-Nuo over 3 years ago - 3 comments

#81 - Report long deletions complying with the VCF format

Pull Request - State: closed - Opened by sposadac about 4 years ago

#81 - Report long deletions complying with the VCF format

Pull Request - State: closed - Opened by sposadac about 4 years ago

#80 - Insertion and deletion on the same haplotype

Issue - State: closed - Opened by zmx21 about 4 years ago - 2 comments

#80 - Insertion and deletion on the same haplotype

Issue - State: closed - Opened by zmx21 about 4 years ago - 2 comments

#79 - List index out of range

Issue - State: closed - Opened by woodford87 about 4 years ago - 3 comments

#79 - List index out of range

Issue - State: closed - Opened by woodford87 about 4 years ago - 3 comments

#78 - Shorah: UnboundLocalError: local variable 'end' referenced before assignment

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

#78 - Shorah: UnboundLocalError: local variable 'end' referenced before assignment

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

#77 - HTSlib 1.10 causes Segfaults

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

#77 - HTSlib 1.10 causes Segfaults

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

#76 - Conda package: no version file

Issue - State: open - Opened by stefanches7 over 4 years ago - 4 comments

#76 - Conda package: no version file

Issue - State: open - Opened by stefanches7 over 4 years ago - 4 comments

#75 - ShoRAH: Illumina reads ; influenza

Issue - State: open - Opened by LauraVP1994 over 4 years ago - 7 comments

#75 - ShoRAH: Illumina reads ; influenza

Issue - State: open - Opened by LauraVP1994 over 4 years ago - 7 comments

#74 - Fix double counting of consensus sequences

Pull Request - State: closed - Opened by sposadac over 4 years ago - 1 comment

#74 - Fix double counting of consensus sequences

Pull Request - State: closed - Opened by sposadac over 4 years ago - 1 comment

#73 - Make discovery of C++ dependencies more robust

Pull Request - State: closed - Opened by kpj over 4 years ago - 1 comment

#73 - Make discovery of C++ dependencies more robust

Pull Request - State: closed - Opened by kpj over 4 years ago - 1 comment

#72 - Conda package for 1.99 not working properly

Issue - State: open - Opened by heylf over 4 years ago - 13 comments

#72 - Conda package for 1.99 not working properly

Issue - State: open - Opened by heylf over 4 years ago - 13 comments

#71 - Multiple fixes to ShoRAH

Pull Request - State: closed - Opened by DrYak over 4 years ago

#71 - Multiple fixes to ShoRAH

Pull Request - State: closed - Opened by DrYak over 4 years ago

#70 - Adding contig info to the metadata in the VCF output file

Pull Request - State: closed - Opened by sposadac over 4 years ago

#70 - Adding contig info to the metadata in the VCF output file

Pull Request - State: closed - Opened by sposadac over 4 years ago

#69 - contig included in VCF meta; base dir path adjusted

Pull Request - State: closed - Opened by NBMueller over 4 years ago

#69 - contig included in VCF meta; base dir path adjusted

Pull Request - State: closed - Opened by NBMueller over 4 years ago

#68 - Make travis happy again

Pull Request - State: closed - Opened by DrYak over 4 years ago - 1 comment

#67 - VCF output implemented

Pull Request - State: closed - Opened by NBMueller over 4 years ago - 9 comments

#67 - VCF output implemented

Pull Request - State: closed - Opened by NBMueller over 4 years ago - 9 comments

#66 - output interpretation

Issue - State: open - Opened by KabitaBaral1 about 5 years ago - 3 comments

#66 - output interpretation

Issue - State: open - Opened by KabitaBaral1 about 5 years ago - 3 comments

#65 - latest version no configure file

Issue - State: closed - Opened by dcm9123 about 5 years ago - 5 comments

#65 - latest version no configure file

Issue - State: closed - Opened by dcm9123 about 5 years ago - 5 comments

#64 - dec.py error "line 582, in main (kp, proposed[kp][0] / proposed[kp][1]))"

Issue - State: closed - Opened by KabitaBaral1 about 5 years ago - 1 comment

#64 - dec.py error "line 582, in main (kp, proposed[kp][0] / proposed[kp][1]))"

Issue - State: closed - Opened by KabitaBaral1 about 5 years ago - 1 comment

#63 - Long reads - nanopore

Issue - State: open - Opened by Psy-Fer about 5 years ago - 5 comments

#63 - Long reads - nanopore

Issue - State: open - Opened by Psy-Fer about 5 years ago - 5 comments

#62 - Fix issue #53 -- "local variable 'prop'"

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

#62 - Fix issue #53 -- "local variable 'prop'"

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

#61 - Error running Shorah.py, and seeking for help

Issue - State: open - Opened by JingniHe over 5 years ago - 2 comments

#61 - Error running Shorah.py, and seeking for help

Issue - State: open - Opened by JingniHe over 5 years ago - 2 comments

#60 - No module named 'shorah_snv'

Issue - State: closed - Opened by yeemey almost 6 years ago - 5 comments

#60 - No module named 'shorah_snv'

Issue - State: closed - Opened by yeemey almost 6 years ago - 5 comments

#59 - results not reproducible even random seed '-S' is set

Issue - State: open - Opened by jeffchen2000 almost 6 years ago - 2 comments

#59 - results not reproducible even random seed '-S' is set

Issue - State: open - Opened by jeffchen2000 almost 6 years ago - 2 comments

#58 - Add SNV as sub-command to the command line and handle errors related to empty windows

Pull Request - State: closed - Opened by sposadac almost 6 years ago - 2 comments

#58 - Add SNV as sub-command to the command line and handle errors related to empty windows

Pull Request - State: closed - Opened by sposadac almost 6 years ago - 2 comments

#57 - overwrite previous results?

Issue - State: open - Opened by jeffchen2000 about 6 years ago - 1 comment

#57 - overwrite previous results?

Issue - State: open - Opened by jeffchen2000 about 6 years ago - 1 comment

#56 - what are the "-----"

Issue - State: closed - Opened by jeffchen2000 about 6 years ago - 1 comment

#56 - what are the "-----"

Issue - State: closed - Opened by jeffchen2000 about 6 years ago - 1 comment

#55 - Allocaholic - the 250 millions malloc killer

Pull Request - State: closed - Opened by DrYak about 6 years ago - 7 comments

#55 - Allocaholic - the 250 millions malloc killer

Pull Request - State: closed - Opened by DrYak about 6 years ago - 7 comments

#54 - Fixing behaviour with indels

Pull Request - State: closed - Opened by DrYak about 6 years ago - 1 comment

#54 - Fixing behaviour with indels

Pull Request - State: closed - Opened by DrYak about 6 years ago - 1 comment

#53 - dec.py: "local variable 'prop' referenced before assignment"

Issue - State: open - Opened by derrickhlin over 6 years ago - 4 comments

#53 - dec.py: "local variable 'prop' referenced before assignment"

Issue - State: open - Opened by derrickhlin over 6 years ago - 4 comments

#52 - With htslib

Pull Request - State: closed - Opened by DrYak over 6 years ago - 24 comments

#52 - With htslib

Pull Request - State: closed - Opened by DrYak over 6 years ago - 24 comments

#51 - Search for executables in PATH

Pull Request - State: closed - Opened by ozagordi over 6 years ago - 4 comments

#51 - Search for executables in PATH

Pull Request - State: closed - Opened by ozagordi over 6 years ago - 4 comments

#50 - handle weird chr in fasta headers - fix issue #32

Pull Request - State: closed - Opened by DrYak over 6 years ago - 8 comments

#50 - handle weird chr in fasta headers - fix issue #32

Pull Request - State: closed - Opened by DrYak over 6 years ago - 8 comments

#49 - New web page

Issue - State: open - Opened by ozagordi over 6 years ago - 3 comments
Labels: help-wanted

#49 - New web page

Issue - State: open - Opened by ozagordi over 6 years ago - 3 comments
Labels: help-wanted

#48 - Restore custom install of exe files

Pull Request - State: closed - Opened by ozagordi over 6 years ago - 13 comments

#48 - Restore custom install of exe files

Pull Request - State: closed - Opened by ozagordi over 6 years ago - 13 comments

#47 - Remove bundled ancient samtools 0.1.19 and move to building against upstream htslib

Issue - State: closed - Opened by SoapZA over 6 years ago - 10 comments
Labels: enhancement

#47 - Remove bundled ancient samtools 0.1.19 and move to building against upstream htslib

Issue - State: closed - Opened by SoapZA over 6 years ago - 10 comments
Labels: enhancement

#46 - Adding gnulib git-version-gen

Pull Request - State: closed - Opened by DrYak over 6 years ago - 1 comment

#46 - Adding gnulib git-version-gen

Pull Request - State: closed - Opened by DrYak over 6 years ago - 1 comment

#45 - Meson switch

Pull Request - State: closed - Opened by ozagordi over 6 years ago - 36 comments

#45 - Meson switch

Pull Request - State: closed - Opened by ozagordi over 6 years ago - 36 comments

#44 - RuntimeError: maximum recursion depth exceeded in cmp

Issue - State: closed - Opened by janoppelt over 6 years ago - 1 comment
Labels: wontfix

#44 - RuntimeError: maximum recursion depth exceeded in cmp

Issue - State: closed - Opened by janoppelt over 6 years ago - 1 comment
Labels: wontfix

#43 - ShoRAH.py error

Issue - State: closed - Opened by woodford87 almost 7 years ago - 2 comments
Labels: wontfix

#43 - ShoRAH.py error

Issue - State: closed - Opened by woodford87 almost 7 years ago - 2 comments
Labels: wontfix

#42 - fixing 'use of uninitialized memory' bug

Pull Request - State: closed - Opened by DrYak almost 7 years ago - 10 comments

#42 - fixing 'use of uninitialized memory' bug

Pull Request - State: closed - Opened by DrYak almost 7 years ago - 10 comments

#41 - weird values in fil output

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

#41 - weird values in fil output

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

#40 - Applying ShoRAH to metagenomic samples

Issue - State: closed - Opened by yorickdevries almost 7 years ago - 3 comments

#40 - Applying ShoRAH to metagenomic samples

Issue - State: closed - Opened by yorickdevries almost 7 years ago - 3 comments

#39 - Shorah throwing error for PacBio bam files

Issue - State: closed - Opened by zusman almost 7 years ago - 3 comments

#39 - Shorah throwing error for PacBio bam files

Issue - State: closed - Opened by zusman almost 7 years ago - 3 comments

#38 - IndexError exception raised due to reads.fas being empty

Issue - State: closed - Opened by terrycojones almost 7 years ago - 3 comments

#38 - IndexError exception raised due to reads.fas being empty

Issue - State: closed - Opened by terrycojones almost 7 years ago - 3 comments

#37 - options `-h`/`--help` should not exit with failure

Pull Request - State: closed - Opened by DrYak about 7 years ago - 5 comments