Ecosyste.ms: Issues

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

GitHub / ACEnglish/truvari issues and pull requests

#229 - Unclear permission denied error when running Truvari bench

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

#228 - is it possible to collapse SVs within known groups

Issue - State: closed - Opened by Han-Cao 3 months ago - 7 comments

#227 - Issue with MAMnet and Truvari Collapse Parameter Optimization

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

#226 - wrong collapse?

Issue - State: closed - Opened by hui-liu 3 months ago - 1 comment

#225 - Collapsed INFO column

Issue - State: closed - Opened by jiadong324 3 months ago - 1 comment

#224 - Question: meaning of the parameter MINHAPLEN

Issue - State: closed - Opened by leone93 3 months ago - 2 comments

#223 - How to handle the "./." genotype in the merged project-level VCF?

Issue - State: closed - Opened by jxcao98 3 months ago - 2 comments

#222 - INFO/END field not carried through from input VCF to output VCF

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

#221 - Q: stratify produces all-zero columns

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

#220 - Same SV failed to merge

Issue - State: closed - Opened by jiadong324 4 months ago - 1 comment

#218 - Truvari Collapse error

Issue - State: closed - Opened by Flooooooooooooower 4 months ago - 1 comment

#214 - Request: truvari collapse --keep option to mantain the ALT sequence

Issue - State: closed - Opened by leone93 6 months ago - 1 comment

#213 - Bug in benchmarking

Issue - State: closed - Opened by rl4940 6 months ago - 4 comments

#212 - Truvari, STRs and Expansion Hunter - Query

Issue - State: closed - Opened by SophieS9 7 months ago - 2 comments

#211 - Suggested minor documentation changes

Issue - State: closed - Opened by nate-d-olson 7 months ago

#210 - Getting same numbers of TP-base and TP-comp

Issue - State: closed - Opened by poddarharsh15 8 months ago - 4 comments

#209 - Allow csi-indexed vcf files

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

#208 - some questions about the results in fp.vcf.gz

Issue - State: closed - Opened by xiaomiyongyuan 8 months ago - 1 comment

#207 - some questions about the results in fp.vcf.gz

Issue - State: closed - Opened by YafeiMaoLab 8 months ago

#206 - Support vector for intra-sample merge

Issue - State: closed - Opened by jiadong324 8 months ago - 6 comments

#205 - md5sum FIPS issue

Issue - State: closed - Opened by shaze 8 months ago - 1 comment

#204 - Unable to run MAFFT

Issue - State: closed - Opened by poddarharsh15 8 months ago - 9 comments

#203 - No FP or TP calls

Issue - State: closed - Opened by jeplb 8 months ago - 2 comments

#201 - merging different SV type?

Issue - State: closed - Opened by leone93 8 months ago - 3 comments

#200 - No TP or FP calls for CNV

Issue - State: closed - Opened by anuravi1234 9 months ago - 1 comment

#199 - GT integrate

Issue - State: closed - Opened by xiaomiyongyuan 9 months ago - 1 comment

#198 - complex genotype problem

Issue - State: closed - Opened by xiaomiyongyuan 9 months ago - 3 comments

#197 - Calculate SNV

Issue - State: closed - Opened by xiaomiyongyuan 9 months ago - 7 comments

#195 - Zero matches between base and comp

Issue - State: closed - Opened by jiadong324 10 months ago - 4 comments

#193 - BED Region off-by-one error

Issue - State: closed - Opened by TimD1 10 months ago - 4 comments

#192 - Update Dockerfile to install dependent python packages.

Pull Request - State: closed - Opened by ctsa 10 months ago - 1 comment

#191 - Update Dockerfile

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

#189 - Failure in pip installation

Issue - State: closed - Opened by jyw-atgithub 10 months ago - 2 comments

#188 - Duplication to Insertion doubt

Issue - State: closed - Opened by poddarharsh15 10 months ago - 4 comments

#187 - TypeError, 'NoneType' and 'NoneType'

Issue - State: closed - Opened by jyw-atgithub 10 months ago - 2 comments

#185 - Truvari refine fails when no regions to refine

Issue - State: closed - Opened by nate-d-olson 11 months ago - 4 comments

#184 - Truvari `refine` doesn't complete

Issue - State: closed - Opened by TimD1 11 months ago - 3 comments

#183 - Pysam bug results in missing info field in output VCF file.

Issue - State: closed - Opened by zhengxinchang 11 months ago - 1 comment

#182 - Truvari bench hangs indefinitely

Issue - State: closed - Opened by TimD1 11 months ago - 3 comments

#181 - Large increase in FNs on pysam v0.22.0

Issue - State: closed - Opened by fennerm 12 months ago - 12 comments

#180 - Error when runnig `truvari bench`

Issue - State: closed - Opened by jyw-atgithub 12 months ago - 2 comments

#179 - One new annotation added by `truvari collapse` ?

Issue - State: closed - Opened by jyw-atgithub 12 months ago - 1 comment

#177 - Unresolved SVs (e.g. ALT=<DEL>)

Issue - State: closed - Opened by poddarharsh15 12 months ago - 8 comments

#176 - Error with VCF file no sample found

Issue - State: closed - Opened by poddarharsh15 about 1 year ago - 4 comments

#175 - Refine Silently killed.

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

#174 - Collapsing results of one sample from multiple SV callers

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

#173 - remap error unrecognized argument `-a`

Issue - State: closed - Opened by nate-d-olson about 1 year ago - 2 comments

#172 - Can Truvari read out query coordinates of duplications from .vcf file?

Issue - State: closed - Opened by 1123231323232 about 1 year ago - 1 comment

#170 - Unable to install because of bwapy wheel build failure on MacOS

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

#168 - TP considered FN

Issue - State: closed - Opened by valeandri about 1 year ago - 5 comments

#167 - Truvari refine hangs indefinitely

Issue - State: closed - Opened by andy941 about 1 year ago - 5 comments

#166 - Truvari phab fails to read VCF headers from output file and crashes

Issue - State: closed - Opened by TimD1 over 1 year ago - 4 comments

#165 - Handling of symbolic variants without ref sequence

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

#160 - Error while installing on macOS M2 (Silica chipset)

Issue - State: closed - Opened by Overcraft90 over 1 year ago - 3 comments

#159 - Are "TP-base" and "TP-comp" always the same value?

Issue - State: closed - Opened by Samvkes over 1 year ago - 1 comment

#158 - Same Variant appears in both TP sets and in FN or FP set.

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

#157 - TypeError: values expected to be 2-tuple, given len=1

Issue - State: closed - Opened by tongyin121 over 1 year ago - 2 comments

#155 - GT-precision calculation

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

#154 - some tests failed on macOS

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

#151 - SVLEN conversion error

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

#150 - Error building Docker image

Issue - State: closed - Opened by Ritu-Kundu over 1 year ago - 1 comment

#148 - Update comparisons.py to sovle the TypeError caused by type of "SVLEN"

Pull Request - State: closed - Opened by PengJia6 over 1 year ago - 1 comment

#147 - Output from truvari bench command

Issue - State: closed - Opened by priyambial123 over 1 year ago - 13 comments

#146 - --choose behavior

Issue - State: closed - Opened by lgmgeo over 1 year ago - 5 comments
Labels: enhancement

#145 - Error with Truvari collapse from bcftools-merged Manta VCFs

Issue - State: closed - Opened by Phillip-a-richmond almost 2 years ago - 1 comment

#142 - Can't install via conda or pip

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

#139 - error from collapse function : TypeError: invalid value for Integer format

Issue - State: closed - Opened by yaowei2010 almost 2 years ago - 2 comments

#138 - query about VCF bed intersection

Issue - State: closed - Opened by prasundutta87 about 2 years ago - 2 comments

#137 - Truvari bench finds no calls in vcf file.

Issue - State: closed - Opened by Irallia about 2 years ago - 5 comments

#136 - Please update collapse wiki

Issue - State: closed - Opened by xiucz about 2 years ago - 1 comment

#135 - A quick query about correlation

Issue - State: closed - Opened by tuannguyen8390 about 2 years ago - 1 comment

#134 - Question about logging in collapse

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

#132 - No TP-base and TP-call match in the benchmark results

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

#131 - Benchmark results in NoneType error

Issue - State: closed - Opened by archmageirvine over 2 years ago - 1 comment

#130 - Conda installation -- issue with header definitions when running truvari

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

#128 - Effects of case on indel comparison

Issue - State: closed - Opened by mnshgl0110 over 2 years ago - 1 comment

#127 - Refactor consistency_report.py

Pull Request - State: closed - Opened by pwwang over 2 years ago - 3 comments

#126 - Use generator instead of list in `create_file_intersections()` to save memory

Pull Request - State: closed - Opened by pwwang over 2 years ago - 4 comments

#125 - KeyError: 'invalid FORMAT: GT' during truvari bench

Issue - State: closed - Opened by mnshgl0110 over 2 years ago - 1 comment

#123 - Invalid argument and BCF warning

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

#122 - ‘truvari collapse -k maxqual‘ does not work for me

Issue - State: closed - Opened by jxcao98 over 2 years ago - 4 comments

#121 - Soft bed regions v2

Pull Request - State: closed - Opened by bnoyvert over 2 years ago - 7 comments

#120 - vcf2df in help message for segment

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

#119 - Reindexing only valid with uniquely valued Index objects

Issue - State: closed - Opened by KasperH2 over 2 years ago - 2 comments

#118 - Clarification needed over the summary.txt file

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

#116 - Clarification of the output (fp.vcf) and the FP field in the summary.txt

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

#115 - truvari anno trf duplicates variants

Issue - State: closed - Opened by noorsmal over 2 years ago - 1 comment

#113 - Extend giab_report.txt with more SV types sorted by size

Issue - State: closed - Opened by KasperH2 over 2 years ago - 1 comment

#112 - refdist flag not working continued

Issue - State: closed - Opened by Addicted-to-coding over 2 years ago - 9 comments

#111 - refdist flag not working

Issue - State: closed - Opened by Addicted-to-coding over 2 years ago - 5 comments

#108 - truvari collapse- inversions and duplications

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