kcleal/dysgu issues and pull requests

#110 - Fix python API default args and call signature

Pull Request - State: closed - Opened by aroon-color about 1 month ago - 1 comment

#109 - Issues when installing with `conda`

Issue - State: open - Opened by jsquaredosquared about 2 months ago - 1 comment

#108 - dysgu_dev <- master

Pull Request - State: closed - Opened by kcleal 2 months ago

#107 - Probably pysam error

Issue - State: closed - Opened by poddarharsh15 2 months ago - 9 comments

#106 - Low SV Count When Performing SV Calling on HG002 ONT Data

Issue - State: closed - Opened by Flooooooooooooower 3 months ago - 4 comments

#105 - Information about running multiple bam files

Issue - State: closed - Opened by poddarharsh15 4 months ago - 3 comments

#104 - `dysgu is not installable because there are no viable options` using Conda

Issue - State: closed - Opened by jsquaredosquared 4 months ago - 2 comments

#103 - updated build process to pyproject.toml

Pull Request - State: closed - Opened by kcleal 4 months ago

#102 - WIP: Add pyproject with setup.py imports for better pip ergonomics

Pull Request - State: closed - Opened by kdm9 4 months ago - 5 comments

#101 - v1.6.6

Pull Request - State: closed - Opened by kcleal 4 months ago

#100 - dsygu filter broken for non-translocations

Issue - State: closed - Opened by kdm9 4 months ago - 4 comments

#99 - correct usage of update_filter_value in filter_normals

Pull Request - State: closed - Opened by kdm9 4 months ago - 1 comment

#98 - Merge pull request #97 from kcleal/master

Pull Request - State: closed - Opened by kcleal 5 months ago

#97 - Merge with master

Pull Request - State: closed - Opened by kcleal 5 months ago

#96 - Dysgu dev

Pull Request - State: closed - Opened by kcleal 5 months ago

#95 - Dysgy v1.6.4

Pull Request - State: closed - Opened by kcleal 5 months ago - 5 comments

#94 - merge master

Pull Request - State: closed - Opened by kcleal 5 months ago

#93 - Issue: Dysgu Module Integration and Empty VCF File Output

Issue - State: closed - Opened by poddarharsh15 5 months ago - 9 comments

#92 - Error with working directories

Issue - State: closed - Opened by poddarharsh15 5 months ago - 10 comments

#91 - using short paired end split reads?

Issue - State: closed - Opened by egnst 5 months ago - 3 comments

#90 - Error installing with conda

Issue - State: closed - Opened by jbruxaux 7 months ago - 6 comments

#89 - Check if input bam file is sorted

Pull Request - State: closed - Opened by JMencius 7 months ago - 4 comments

#88 - Paired-end reads calling sv

Issue - State: closed - Opened by C-YONG 8 months ago - 6 comments

#87 - v1.6.3

Pull Request - State: closed - Opened by kcleal 8 months ago

#86 - Process_KILLED

Issue - State: closed - Opened by poddarharsh15 8 months ago - 7 comments

#85 - Parameters for R9 Guppy2, 4, 6

Issue - State: closed - Opened by StellariaYuki 9 months ago - 4 comments

#84 - Long run time

Issue - State: closed - Opened by JMencius 9 months ago - 13 comments

#83 - When merging a large number of samples, the process is very slow

Issue - State: closed - Opened by zhongleishi 9 months ago

#82 - When combining a large number of samples, the speed is very slow

Issue - State: closed - Opened by zhongleishi 9 months ago - 13 comments

#81 - TypeError: an integer is required when using --sites option and manta.vcf

Issue - State: closed - Opened by bbunce 9 months ago - 6 comments

#80 - Subject: Inquiry on Benchmarking DEL and INS Events with dysgu Pipelines.

Issue - State: closed - Opened by poddarharsh15 11 months ago - 35 comments

#79 - _pickle.UnpicklingError: invalid load key, 'A'. Failed to read from standard input: unknown file type

Issue - State: closed - Opened by wenyuhaokikika 11 months ago - 2 comments

#78 - Getting SV length in dysgu output vcf

Issue - State: closed - Opened by TizianaS92 12 months ago - 3 comments

#77 - clarification needed on RG and samples

Issue - State: closed - Opened by warthmann 12 months ago - 4 comments

#76 - problems genotyping, dysgu run --sites

Issue - State: closed - Opened by warthmann 12 months ago - 3 comments

#75 - Fixed multiple "/" in filename when using stdin in main.py

Pull Request - State: closed - Opened by kearseya about 1 year ago

#74 - Update filter_normals.py

Pull Request - State: closed - Opened by kearseya about 1 year ago

#73 - Got an warning when Loading Model in "dysgu run"

Issue - State: closed - Opened by LNGDingj about 1 year ago - 1 comment

#72 - When will docker image with new release be available?

Issue - State: closed - Opened by LNGDingj about 1 year ago - 1 comment

#71 - v1.6.1

Pull Request - State: closed - Opened by kcleal about 1 year ago

#70 - long reads default mapq lowered to 1: help text for dysgu call still says pacbio and nanopore mode has --mq 20

Issue - State: closed - Opened by tbenavi1 about 1 year ago - 1 comment

#69 - Dysgu filter IndexError: string index out of range

Issue - State: closed - Opened by tbenavi1 about 1 year ago - 6 comments

#68 - OverflowError: can't convert negative value to size_t

Issue - State: closed - Opened by wenyuhaokikika about 1 year ago - 2 comments

#67 - v1.6.0

Pull Request - State: closed - Opened by kcleal over 1 year ago

#66 - Run OSError: [Errno 24] Too many open files Mac OS M

Issue - State: closed - Opened by husamia over 1 year ago - 4 comments

#65 - Generating Alternative Reference

Issue - State: closed - Opened by grpiccoli over 1 year ago - 16 comments
Labels: help wanted, question

#64 - Error with --search option

Issue - State: closed - Opened by husamia over 1 year ago - 11 comments

#63 - what is SVLEN？

Issue - State: closed - Opened by wenyuhaokikika over 1 year ago - 2 comments

#62 - no command as dysgu filter-normal

Issue - State: closed - Opened by GManjiLab over 1 year ago - 3 comments

#61 - GT value for missing data

Issue - State: closed - Opened by linsson over 1 year ago - 4 comments

#60 - ValueError: numpy.ufunc size changed, may indicate binary incompatibility. Expected 232 from C header, got 216 from PyObject

Issue - State: closed - Opened by zengxi-hada over 1 year ago - 8 comments

#59 - Support for Python 3.11

Issue - State: closed - Opened by tbenavi1 over 1 year ago - 2 comments

#58 - input bam files refinements

Issue - State: closed - Opened by linsson over 1 year ago - 2 comments

#57 - Can dysgu be used in haploid genome?

Issue - State: closed - Opened by wushyer over 1 year ago - 5 comments

#56 - Segfault only when using --regions and not --contigs False

Issue - State: closed - Opened by moraglewis over 1 year ago - 6 comments

#55 - Merging samples VCFs

Issue - State: closed - Opened by mkohailan over 1 year ago - 8 comments

#54 - AttributeError: module 'numpy' has no attribute 'float'

Issue - State: closed - Opened by xiekunwhy over 1 year ago - 2 comments

#53 - somatic filter sv script

Pull Request - State: closed - Opened by kearseya over 1 year ago

#52 - About Pacio ccs.bam

Issue - State: closed - Opened by ClarenceHsiang almost 2 years ago - 1 comment

#51 - Type error: '<' not supported between instances of 'bool' and 'str'

Issue - State: closed - Opened by distilledchild almost 2 years ago - 26 comments
Labels: bug

#50 - RAM Issue - merging large cohorts

Issue - State: closed - Opened by lurens almost 2 years ago - 14 comments

#49 - Error while trying to clone the repository

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

#48 - Bug in re-mapping?

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

#47 - Merging genotype files

Issue - State: closed - Opened by arunvv90 over 2 years ago - 7 comments

#46 - Hi,

Issue - State: closed - Opened by arunvv90 over 2 years ago

#45 - Invalid character '.' in 'GQ' FORMAT field

Issue - State: closed - Opened by arunvv90 over 2 years ago - 5 comments

#44 - Multiprocessing error

Issue - State: closed - Opened by mc-er over 2 years ago - 14 comments

#43 - SV calling NOT working

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

#42 - re-using temp files with --ibam

Issue - State: closed - Opened by husamia over 2 years ago - 4 comments
Labels: question

#41 - Merging SV from Oxford Nanopore - expected runtime

Issue - State: closed - Opened by agolicz over 2 years ago - 3 comments

#40 - changing default argument when high read depth

Issue - State: closed - Opened by splaisan over 2 years ago - 5 comments

#39 - running docker container fails

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

#38 - input vcf cannot be read

Issue - State: closed - Opened by nponts over 2 years ago - 2 comments
Labels: documentation, question

#37 - Best protocol about dysgu run/merge with WGS 35X from multiple patients? Calling cohorts

Issue - State: closed - Opened by Taalouane over 2 years ago - 8 comments
Labels: documentation, question

#36 - Error running 1.3.10

Issue - State: closed - Opened by holtjma over 2 years ago - 3 comments
Labels: enhancement

#35 - PacBio CLR reads failing with Nanopore setting

Issue - State: closed - Opened by AQWixom over 2 years ago - 4 comments

#34 - TRA variants

Issue - State: closed - Opened by Akazhiel over 2 years ago - 5 comments
Labels: enhancement

#33 - Read Depth

Issue - State: closed - Opened by Akazhiel over 2 years ago - 1 comment
Labels: question

#32 - Error with --max-cov auto

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

#31 - Error - pip3 dysgu installation

Issue - State: closed - Opened by KristinaGagalova over 2 years ago - 5 comments

#30 - linux-debs install

Pull Request - State: closed - Opened by kearseya over 2 years ago

#29 - Installation "fixes"

Pull Request - State: closed - Opened by kearseya over 2 years ago - 1 comment

#28 - Dysgu Cluster

Issue - State: closed - Opened by assane-mbodj over 2 years ago - 3 comments
Labels: question

#27 - PacBio long reads?

Issue - State: closed - Opened by beantkapoor786 over 2 years ago - 3 comments
Labels: enhancement, wontfix

#26 - Reporting only SVs from --sites for genotyping

Issue - State: closed - Opened by wbooker almost 3 years ago - 3 comments
Labels: enhancement

#25 - redundant results and insertion variants recording

Issue - State: closed - Opened by biozzq almost 3 years ago - 3 comments
Labels: bug

#24 - Manual installation

Issue - State: closed - Opened by colindaven almost 3 years ago - 4 comments
Labels: documentation

#23 - Pickle Warning in run command

Issue - State: closed - Opened by nickhsmith almost 3 years ago - 1 comment
Labels: wontfix

#22 - Does the merge command work for translocations?

Issue - State: closed - Opened by tbenavi1 almost 3 years ago - 7 comments

#21 - Installation Note

Issue - State: closed - Opened by nickhsmith almost 3 years ago - 38 comments
Labels: documentation

#20 - Location on CHR2 for translocations

Issue - State: closed - Opened by tbenavi1 almost 3 years ago - 2 comments
Labels: bug, enhancement

#19 - Coverage of reads

Issue - State: closed - Opened by arunvv90 almost 3 years ago - 7 comments
Labels: question

#18 - Supporting reads

Issue - State: closed - Opened by RenzoTale88 almost 3 years ago - 6 comments
Labels: enhancement

GitHub / kcleal/dysgu issues and pull requests