Ecosyste.ms: Issues

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GitHub / molgenis/VaSeBuilder issues and pull requests

#114 - Updated Ygor and added protocol

Pull Request - State: open - Opened by MatthieuBeukers about 4 years ago - 1 comment

#113 - Add option to slice donors without an acceptor

Issue - State: open - Opened by TDMedina over 4 years ago
Labels: enhancement

#112 - Patch to fix version number.

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

#111 - Doc updates

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

#110 - Update docs, add flowcharts

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

#109 - Doc updates.

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

#108 - Update some documentation

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

#107 - Restructured repository for PyPi and pip compatibility.

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

#106 - Remove old flowcharts, update documentation

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

#105 - Updated docs.

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

#104 - Documentation updates 11-06-2020 and on

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

#103 - Documentation 08-06-2020 update

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

#102 - Switched to ReadTheDocs theme for MkDocs.

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

#101 - Fix mistake in new readme.

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

#100 - Updated documentation.

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

#99 - New Readme

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

#98 - Typo in help menu for --seed argument default

Issue - State: closed - Opened by TDMedina over 4 years ago - 1 comment
Labels: bug

#97 - Add first version of some documentation files

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

#96 - WIP to master in preperation for new release.

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

#95 - Change pip to python -m pip

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

#94 - Latest updates to WIP branch.

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

#93 - Add filter list (e.g. MVL) fields to VCF output INFO field

Issue - State: open - Opened by TDMedina almost 5 years ago
Labels: enhancement

#92 - Argument parsing overhaul with related changes for expanded functionality.

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

#91 - Change logging outputs

Issue - State: closed - Opened by TDMedina almost 5 years ago
Labels: enhancement

#90 - Identify sample sex for sex chromosome variants from genotype ploidy.

Issue - State: open - Opened by TDMedina almost 5 years ago
Labels: enhancement

#89 - BAM header merging broken in D-mode bam output

Issue - State: closed - Opened by TDMedina almost 5 years ago
Labels: bug

#88 - Index_out doesn't work

Issue - State: closed - Opened by TDMedina almost 5 years ago
Labels: bug

#87 - Check for BAM indexes in paramchecker

Issue - State: closed - Opened by TDMedina almost 5 years ago
Labels: enhancement

#86 - Lynting, Refactoring, and Bug Fixes

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

#85 - Output FASTQ donor reads from BAM are all forward direction.

Issue - State: closed - Opened by TDMedina almost 5 years ago
Labels: bug

#84 - D-mode BAM output and other updates/changes

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

#83 - Implementation of new 'Sample' data object and ID hashing.

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

#82 - Variant filtering is wonky.

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

#81 - Added utils.

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

#80 - Implement usage of pysam.VariantRecord

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

#79 - Hierarchical tree for selecting variants to include into a set.

Issue - State: open - Opened by TDMedina over 5 years ago
Labels: enhancement

#78 - Consider grouping variants from the same gene from the same sample.

Issue - State: open - Opened by TDMedina over 5 years ago - 1 comment
Labels: enhancement

#77 - Fix F-mode, add write config file when cli parameters are used

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

#76 - Parallel FastQ writing in AC mode.

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

#75 - Parallelized FastQ writing.

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

#74 - Output config file when command line parameters are used

Issue - State: closed - Opened by MatthieuBeukers over 5 years ago - 1 comment
Labels: enhancement

#73 - Merge working Beta branch into Master for new release.

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

#72 - Utils: Use variant context file to subset VCF/BCF

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

#71 - Implement filter based on specified column and value for variant filter list (mvl)

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

#70 - Output fixes, AC-mode semi random read distribution

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

#69 - Fix missing FastQ mates and hardclipped reads.

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

#68 - Samples not included in an MVL filter list are not skipped.

Issue - State: closed - Opened by TDMedina over 5 years ago - 1 comment
Labels: bug

#67 - Unmapped mate not added to P-mode FQ output.

Issue - State: closed - Opened by TDMedina over 5 years ago - 1 comment
Labels: bug

#66 - Missing newlines and,data in debug files

Issue - State: closed - Opened by TDMedina over 5 years ago - 1 comment
Labels: bug

#65 - BVCS bug in overlapping contexts

Issue - State: closed - Opened by TDMedina over 5 years ago - 1 comment
Labels: bug

#64 - Multi-base, multi-allele variants sometimes have different positions in the filtering list vs. original VCF.

Issue - State: closed - Opened by TDMedina over 5 years ago - 2 comments
Labels: help wanted

#63 - Implement usage of -s/--seed parameter

Issue - State: closed - Opened by MatthieuBeukers over 5 years ago - 1 comment
Labels: enhancement

#62 - Add VaSeBuilder uuid to other context output files

Issue - State: closed - Opened by MatthieuBeukers over 5 years ago
Labels: enhancement

#61 - Reverse acceptor filtering logic to increase speed.

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

#60 - Missing variant ID's from debug log.

Issue - State: closed - Opened by TDMedina over 5 years ago - 1 comment
Labels: bug

#59 - Check acceptor/donor context id before adding to variant context

Issue - State: open - Opened by MatthieuBeukers over 5 years ago
Labels: enhancement

#58 - Create linkfile between variant contexts and fastq output files

Issue - State: closed - Opened by MatthieuBeukers over 5 years ago - 1 comment
Labels: enhancement

#57 - Add method to use a mapping table to change sample names

Issue - State: closed - Opened by MatthieuBeukers over 5 years ago - 1 comment
Labels: enhancement

#56 - Add sanity checks during the run

Issue - State: open - Opened by MatthieuBeukers over 5 years ago
Labels: enhancement

#55 - Implement specific runmodes in their own separate methods

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

#54 - Patches for latest update.

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

#53 - Add donor fastq reads semi randomly over the acceptors

Issue - State: closed - Opened by MatthieuBeukers over 5 years ago - 1 comment
Labels: enhancement

#52 - Acceptor reads not filtered properly in AC mode.

Issue - State: closed - Opened by TDMedina over 5 years ago - 1 comment
Labels: bug

#51 - FastQ R1 files are being written twice in AC mode.

Issue - State: closed - Opened by TDMedina over 5 years ago - 1 comment
Labels: bug

#50 - Add command used to output log.

Issue - State: closed - Opened by TDMedina over 5 years ago - 1 comment
Labels: enhancement

#49 - Using gender-mismatched donor/acceptors makes validation difficult.

Issue - State: open - Opened by TDMedina over 5 years ago
Labels: enhancement

#48 - Add first methods for adding existing donor fastq files

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

#47 - Major addition of multiple modes.

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

#45 - Start vasebuilder from an existing variant context file.

Issue - State: closed - Opened by TDMedina over 5 years ago - 1 comment
Labels: enhancement

#44 - Modified method to return only unique reads.

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

#43 - Duplicate fastq records.

Issue - State: closed - Opened by TDMedina over 5 years ago - 1 comment
Labels: bug

#42 - Implement check that variant contexts themselves do not overlap

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

#41 - Small updates to unittests

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

#40 - First fix for using CRAM files

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

#39 - Use reference when opening alignment files

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

#38 - CRAM cache files are output to user's home directory.

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

#37 - Updates to unittests

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

#36 - Small bugfix.

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

#35 - Allow users to supply a configuration file

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

#33 - Replaced missing argparse line for donor_only.

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

#32 - Use a listing file for BAM/CRAM donor files to use

Issue - State: closed - Opened by MatthieuBeukers over 5 years ago - 1 comment
Labels: enhancement

#31 - Use of 'chr' for chromosomes

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

#30 - Fixed acceptor exclusions.

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

#29 - Add support for CRAM files

Issue - State: closed - Opened by MatthieuBeukers over 5 years ago
Labels: enhancement

#28 - Small updates, add command line parameter to vase.py

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

#27 - Missing records in position stats files.

Issue - State: closed - Opened by TDMedina over 5 years ago - 1 comment
Labels: bug

#26 - Large changes to VaSeBuilder to expand features.

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

#25 - add check for acceptor reads > 0

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

#24 - Added outlier checking for variant context determination.

Pull Request - State: closed - Opened by TDMedina over 5 years ago
Labels: enhancement

#23 - Update to vaseutils and issue fix

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

#22 - Catch errors in establishing variant context when no reads are found in BAM file.

Issue - State: closed - Opened by TDMedina over 5 years ago - 2 comments
Labels: bug

#21 - Change debug delimiters to tabs.

Issue - State: closed - Opened by TDMedina over 5 years ago - 1 comment
Labels: enhancement

#20 - Added option to output donor fastq files only, without acceptor fastqs.

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

#19 - Update to make VaSeBuilder faster, update to VaSeUtils

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

#18 - Added option to prevent fastq output.

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

#17 - New mate method in master

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

#16 - Fixed bad dictionary key reference.

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

#4 - Not currently compatible with BCF files

Issue - State: closed - Opened by TDMedina over 5 years ago - 1 comment
Labels: enhancement