Ecosyste.ms: Issues

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

GitHub / iqbal-lab-org/minos issues and pull requests

#124 - bug fix --filter_min_frs should be float

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

#123 - no loop devices available

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

#122 - Update gramtools

Pull Request - State: closed - Opened by martinghunt about 2 years ago

#121 - Gramtools ee98085fbb9d8be5afd2288424c3d6dded796ab8

Pull Request - State: closed - Opened by martinghunt about 2 years ago

#120 - Variants at contig ends

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

#119 - Compatibility issues between minos' gramtools.py script and gramtools' command

Issue - State: closed - Opened by ycode-sh over 2 years ago - 41 comments

#118 - Add test data

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

#117 - Ignore all non-ACGT alleles from input VCF files

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

#116 - How to build a manifest.tsv file. Can you provide a sample file?

Issue - State: open - Opened by joybio over 2 years ago - 18 comments

#115 - i don't know error

Issue - State: open - Opened by kdyoung100 over 2 years ago - 4 comments

#114 - GitHub actions instead of travis

Pull Request - State: closed - Opened by martinghunt about 3 years ago

#113 - Fixed #112. Added libjpeg-dev to dependencies

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

#112 - Missing jpeg library when building the Singularity image

Issue - State: closed - Opened by jordivea-odap over 3 years ago

#111 - Depth tags and filter fixes

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

#110 - Install for minos is broken gramtools dependency issue

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

#109 - Negative binomial fixes

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

#108 - Fixes to handle when non-ACGT is in ref fasta

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

#107 - Add opt to make distance matrix at end of regeno pipeline

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

#106 - Regeno filter samples

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

#105 - Regeno improvements

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

#104 - Genotyping distributions fixes

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

#103 - Remove precision and recall code. No longer used

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

#102 - Change default VCF filters

Pull Request - State: closed - Opened by martinghunt almost 5 years ago

#101 - Default homozygous calling

Pull Request - State: closed - Opened by martinghunt almost 5 years ago

#100 - Write contig header lines to final vcf

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

#99 - Add contig header lines to final.vcf

Issue - State: closed - Opened by martinghunt about 5 years ago

#98 - Dump binary encoded genotypes after regenotyping

Issue - State: open - Opened by iqbal-lab about 5 years ago - 3 comments
Labels: enhancement

#97 - Disable plots made by minos adjudicate

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

#96 - Genotyping refactoring and fix diploid coverage collection

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

#95 - multi sample pipeline is broken if not splitting the VCFs

Issue - State: closed - Opened by martinghunt about 5 years ago

#94 - Do not cluster adjacent variants

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

#93 - Add travis and singularity

Pull Request - State: closed - Opened by martinghunt about 5 years ago - 2 comments

#92 - Call filtering

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

#91 - Update gramtools

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

#90 - Ignore bad vcf pos

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

#89 - Vcf fixes

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

#88 - Stop if too many variants

Issue - State: closed - Opened by martinghunt about 5 years ago

#87 - Speed up genotyping

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

#86 - Speed up genotyping

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

#84 - Try to make valid VCF file

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

#83 - General tidying up

Pull Request - State: closed - Opened by martinghunt over 5 years ago

#82 - Add singularity container file

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

#81 - Use entry points

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

#80 - Make unit tests discoverable

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

#79 - Math error during genotyping

Issue - State: closed - Opened by bricoletc over 5 years ago
Labels: bug

#78 - Null genotypes missing GT_CONF_PERCENTILE value

Issue - State: closed - Opened by mbhall88 over 5 years ago - 6 comments
Labels: bug

#77 - Invalid DP FORMAT header

Issue - State: closed - Opened by mbhall88 over 5 years ago - 5 comments
Labels: bug

#76 - removing perl_generated_vcf caused a bug

Issue - State: closed - Opened by iqbal-lab over 5 years ago - 3 comments

#74 - hardcoded ram limit for one step of multisample workflow

Issue - State: closed - Opened by iqbal-lab over 5 years ago

#73 - Parallelised build in nextflow

Pull Request - State: closed - Opened by bricoletc over 5 years ago - 9 comments

#72 - multi-sample pipeline: parallelise (nextflow) chunk building

Issue - State: closed - Opened by iqbal-lab over 5 years ago - 3 comments

#71 - Do not use unmapped reads in split pipeline

Pull Request - State: closed - Opened by martinghunt almost 6 years ago

#70 - Implement filtering

Pull Request - State: closed - Opened by martinghunt almost 6 years ago

#69 - multi sample pipeline: ALT allele list in final VCF differ between samples/files

Issue - State: closed - Opened by kerrimalone almost 6 years ago - 7 comments

#68 - Filter on depth and gt conf percentile

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

#67 - Option to not use unmapped reads in multi sample pipeline

Issue - State: closed - Opened by martinghunt almost 6 years ago - 2 comments

#66 - Check if whitespace in seq names breaks minos

Issue - State: closed - Opened by martinghunt almost 6 years ago - 2 comments

#65 - Call filtering

Pull Request - State: closed - Opened by martinghunt almost 6 years ago

#64 - Add Ns to flanks when evaluating recall to avoid issues where truth p…

Pull Request - State: closed - Opened by rmcolq almost 6 years ago

#62 - Fix off by one error reading BED files

Pull Request - State: closed - Opened by martinghunt almost 6 years ago

#61 - Check with ref improvements

Pull Request - State: closed - Opened by martinghunt almost 6 years ago

#60 - Fix tests for cluster_vcf_records 0.9.1

Pull Request - State: closed - Opened by martinghunt almost 6 years ago

#59 - Call filtering

Pull Request - State: closed - Opened by martinghunt almost 6 years ago

#58 - add `max_soft_clipped parameter` to recall functions

Pull Request - State: closed - Opened by rmcolq almost 6 years ago

#57 - Tidy test files and prints

Pull Request - State: closed - Opened by martinghunt about 6 years ago

#56 - Fix mask

Pull Request - State: closed - Opened by rmcolq about 6 years ago

#55 - Add allow ref alleles option

Pull Request - State: closed - Opened by rmcolq about 6 years ago

#54 - use gramtools build --all-kmers. Default k=10. Use k=5 for tests

Pull Request - State: closed - Opened by martinghunt over 6 years ago

#53 - Save ram multi pipeline cluster

Pull Request - State: closed - Opened by martinghunt over 6 years ago

#52 - Bug fixes if only TPs or FPs found

Pull Request - State: closed - Opened by martinghunt over 6 years ago

#51 - Add dp and gt conf plots

Pull Request - State: closed - Opened by martinghunt over 6 years ago

#50 - quasimap use --output-directory instead of --run-directory

Pull Request - State: closed - Opened by martinghunt over 6 years ago

#49 - Check with ref use edit distance

Pull Request - State: closed - Opened by martinghunt over 6 years ago

#48 - gramtools quasimap `--run-directory` deprecated

Issue - State: closed - Opened by martinghunt over 6 years ago

#47 - Speedup bcftools merge

Pull Request - State: closed - Opened by martinghunt over 6 years ago

#46 - remove cortex MISMAPPED_UNPLACEABLE VCF records

Issue - State: open - Opened by martinghunt over 6 years ago - 1 comment

#45 - Exclude regions to verify

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#44 - if chunking VCF, check bam is indexed

Issue - State: open - Opened by martinghunt almost 7 years ago

#43 - Gramtools build tweaks

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#42 - Multithread vcf chunker

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#41 - Implement multithreading gramtools build vcf chunks

Issue - State: closed - Opened by martinghunt almost 7 years ago

#40 - split by allele count

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#39 - Multi sample keep zero cov

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#38 - multi sample pipeline keep zero cov alleles

Issue - State: closed - Opened by martinghunt almost 7 years ago

#37 - Gramtools error checking

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#36 - Add max_alleles_per_cluster option

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#35 - stop if not running anything

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#34 - Logging improvements

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#33 - Remove zero cov alleles

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#32 - Chunk variants

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#31 - Implement chunking the reference genome

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

#30 - multi_sample_pipeline limit max alleles

Issue - State: closed - Opened by martinghunt almost 7 years ago

#29 - multi_sample_pipeline --norun FileNotFoundError

Issue - State: closed - Opened by martinghunt almost 7 years ago

#27 - Logging issues

Issue - State: closed - Opened by martinghunt almost 7 years ago

#26 - Multi sample filter vcf

Pull Request - State: closed - Opened by martinghunt almost 7 years ago

#25 - Nextflow memory options

Pull Request - State: closed - Opened by martinghunt almost 7 years ago