Ecosyste.ms: Issues

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

GitHub / cytham/nanovar issues and pull requests

#99 - v1.8.3

Pull Request - State: closed - Opened by cytham about 1 month ago

#98 - V1.8.2

Pull Request - State: closed - Opened by cytham about 1 month ago

#97 - Modify README hyperlink

Pull Request - State: closed - Opened by cytham about 2 months ago

#96 - Update README.md

Pull Request - State: closed - Opened by asmmahmoud about 2 months ago

#95 - Update README.md

Pull Request - State: closed - Opened by asmmahmoud about 2 months ago

#94 - ModuleNotFoundError: No module named 'nanovar.nv_bam_parser'

Issue - State: closed - Opened by 0Bernhard 3 months ago - 1 comment

#93 - Missing AS tag

Issue - State: open - Opened by kcleal 3 months ago - 1 comment

#92 - v1.8.1

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

#91 - v1.8.0 update

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

#89 - bedtools getfasta error

Issue - State: open - Opened by C-YONG 7 months ago - 17 comments

#87 - Add alt seq and cram support

Pull Request - State: closed - Opened by cytham 9 months ago

#86 - Add alt seq and cram support

Pull Request - State: closed - Opened by cytham 9 months ago

#85 - Upgrade to v1.6.2

Pull Request - State: closed - Opened by benoukraflab 10 months ago

#84 - Upgrade to v1.6.2

Pull Request - State: closed - Opened by benoukraflab 10 months ago

#83 - Upgrade to v1.6.2

Pull Request - State: closed - Opened by AsmaaSamyMohamedMahmoud 10 months ago

#82 - V1.6.2

Pull Request - State: closed - Opened by cytham 10 months ago

#81 - Alternative sequence in VCF

Issue - State: closed - Opened by jiadong324 10 months ago - 6 comments

#80 - Bump pillow from 10.2.0 to 10.3.0

Pull Request - State: closed - Opened by dependabot[bot] 11 months ago - 3 comments
Labels: dependencies, python

#79 - v1.6.1 - restrict tf<=2.15.1

Pull Request - State: closed - Opened by cytham 11 months ago

#78 - tensorflow 2.16 incompatibility

Pull Request - State: closed - Opened by cytham 11 months ago

#76 - update conda version

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

#75 - Not finding 4kb deletion

Issue - State: closed - Opened by ccbruels about 1 year ago - 3 comments

#74 - v1.6.0

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

#73 - Bump fonttools from 4.42.1 to 4.43.0

Pull Request - State: closed - Opened by dependabot[bot] about 1 year ago - 1 comment
Labels: dependencies, python

#71 - IndexError : list index out of range

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

#70 - Removed maxovl filter

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

#69 - Fix cytocad import bug

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

#68 - cytocad is not listed as a dependency for nanovar:1.5.0

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

#67 - module 'numpy' has no attribute 'object'.

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

#66 - Bump werkzeug from 2.3.7 to 3.0.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, python

#65 - Bump urllib3 from 1.26.16 to 1.26.18

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, python

#64 - Bump pillow from 10.0.0 to 10.0.1

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies, python

#63 - Bump urllib3 from 1.26.16 to 1.26.17

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies, python

#62 - Workflow failing due to makeblastdb and hs-blastn

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

#60 - cram file support

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

#59 - interpreting output (SVLEN)

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

#58 - Error: windowmasker obinary failed

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

#57 - Bump werkzeug from 2.0.1 to 2.2.3

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies, python

#56 - Bump oauthlib from 3.1.1 to 3.2.2

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies, python

#55 - TypeError: Error: Genome filter BED contig id not found in reference at line 1

Issue - State: closed - Opened by egnst about 2 years ago - 6 comments

#54 - Bump certifi from 2021.5.30 to 2022.12.7

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies, python

#53 - Bump pillow from 8.3.2 to 9.3.0

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies, python

#52 - Bump tensorflow-cpu from 2.6.0 to 2.9.3

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago - 1 comment
Labels: dependencies, python

#51 - Bump protobuf from 3.17.3 to 3.18.3

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies, python

#50 - Bump oauthlib from 3.1.1 to 3.2.1

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies, python

#49 - HTML Report Figure's Aren't Showing

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

#48 - can nanovar work on incomplete genomes?

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

#47 - Bump numpy from 1.19.5 to 1.22.0

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#46 - Bump tensorflow-cpu from 2.6.0 to 2.7.2

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#45 - Bump tensorflow-cpu from 2.6.0 to 2.6.4

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#44 - Bump pillow from 8.3.2 to 9.0.1

Pull Request - State: closed - Opened by dependabot[bot] almost 3 years ago - 1 comment
Labels: dependencies

#43 - Unable to install using conda

Issue - State: closed - Opened by beantkapoor786 almost 3 years ago - 4 comments

#42 - Bump tensorflow-cpu from 2.6.0 to 2.6.3

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#41 - Error: Unrecognized CIGAR translated symbol "3"

Issue - State: closed - Opened by infotmatician about 3 years ago - 2 comments

#40 - Bump pillow from 8.3.2 to 9.0.0

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago - 1 comment
Labels: dependencies

#39 - Bump tensorflow-cpu from 2.6.0 to 2.6.1

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#38 - After run nanovar, we cannot get the vcf results, could you give some advice?

Issue - State: closed - Opened by zch0803 over 3 years ago - 6 comments

#37 - Corrected the minimap2 pacbio preset bug in nanovar/nv_align.py

Pull Request - State: closed - Opened by LYC-vio over 3 years ago

#36 - Nanovar does not parse -x correctly when utilizing minimap2

Issue - State: closed - Opened by LYC-vio over 3 years ago - 3 comments

#35 - output does not match input data

Issue - State: closed - Opened by MeiShu00 over 3 years ago - 4 comments

#34 - Dev

Pull Request - State: closed - Opened by cytham over 3 years ago

#33 - Bump pillow from 8.3.1 to 8.3.2

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#32 - v1.4.0 update

Pull Request - State: closed - Opened by cytham over 3 years ago

#31 - Bump tensorflow from 2.4.1 to 2.5.1

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#30 - Bump tensorflow-cpu from 2.4.1 to 2.5.1

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#29 - CRITICAL - Error: hs-blastn alignment failed

Issue - State: closed - Opened by MingchenInSZ over 3 years ago - 10 comments

#28 - AttributeError: 'str' object has no attribute 'decode'

Issue - State: closed - Opened by gchevignon over 3 years ago - 41 comments

#27 - Bump urllib3 from 1.24.2 to 1.26.5

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago
Labels: dependencies

#26 - Bump tensorflow from 2.4.1 to 2.5.0

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#25 - "Exeption: Read has none or more than 2 clusters" error

Issue - State: closed - Opened by kristinastenlokk almost 4 years ago - 5 comments

#24 - Why sv_support_read contains reads from other chromosome?

Issue - State: closed - Opened by yekaizhou almost 4 years ago - 3 comments

#23 - Bump rsa from 4.0 to 4.7

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#22 - sv_cluster() Error

Issue - State: closed - Opened by kztyes almost 4 years ago - 12 comments

#21 - Bump rsa from 4.0 to 4.1

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 1 comment
Labels: dependencies

#20 - Bump tensorflow from 2.3.1 to 2.4.0

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago
Labels: dependencies

#19 - Nanovar fails with Python KeyError when clustering breakends

Issue - State: closed - Opened by oneillkza almost 4 years ago - 5 comments

#18 - Nanovar segfaults on Neural network inference stage

Issue - State: closed - Opened by oneillkza almost 4 years ago - 15 comments

#17 - Bump cryptography from 3.2 to 3.3.2

Pull Request - State: closed - Opened by dependabot[bot] about 4 years ago
Labels: dependencies

#16 - Bump tensorflow from 2.1.0 to 2.3.1

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago
Labels: dependencies

#15 - Bump cryptography from 2.8 to 3.2

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago
Labels: dependencies

#14 - Bump tensorflow from 2.1.0 to 2.1.2

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#13 - raise Exception("Read %s has none or more than 2 clusters" % read)

Issue - State: closed - Opened by yuntwang over 4 years ago - 6 comments

#12 - OMP: Error #15: Initializing libomp.so

Issue - State: closed - Opened by umahsn over 4 years ago - 2 comments
Labels: duplicate

#11 - Failure when generating HTML report

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

#10 - Intersecting NanoVar SVs

Issue - State: closed - Opened by asmariyaz23 almost 5 years ago - 1 comment

#9 - Nanovar makeblastdb failed

Issue - State: closed - Opened by jiadong324 almost 5 years ago - 36 comments

#8 - How to use nanovar to do population-scale SV calling?

Issue - State: closed - Opened by xiekunwhy almost 5 years ago - 2 comments

#7 - hs-blastn alignment failed

Issue - State: closed - Opened by zihhuafang almost 5 years ago - 27 comments

#6 - IndexError: list index out of range

Issue - State: closed - Opened by Tintest about 5 years ago - 11 comments
Labels: bug

#5 - Error loading vcf file into IGV

Issue - State: closed - Opened by jagos01 about 5 years ago - 8 comments
Labels: bug

#4 - Run fails at nv_cluster.py IndexError: list index out of range

Issue - State: closed - Opened by asmariyaz23 about 5 years ago - 4 comments

#3 - Updated README.md

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

#2 - Annotating variants called by NanoVar

Issue - State: closed - Opened by asmariyaz23 about 5 years ago - 1 comment

#1 - Boundaries does not match error

Issue - State: closed - Opened by asmariyaz23 about 5 years ago - 5 comments
Labels: bug