molgenis VaSeBuilder issues

molgenis / VaSeBuilder

Validation Set Builder

GNU Lesser General Public License v3.0

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issues

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Updated Ygor and added protocol

#114 MatthieuBeukers opened 3 years ago
1
Add option to slice donors without an acceptor

#113 TDMedina opened 4 years ago
0
Patch to fix version number.

#112 TDMedina closed 4 years ago
1
Doc updates

#111 TDMedina closed 4 years ago
0
Update docs, add flowcharts

#110 MatthieuBeukers closed 4 years ago
0
Doc updates.

#109 TDMedina closed 4 years ago
0
Update some documentation

#108 MatthieuBeukers closed 4 years ago
0
Restructured repository for PyPi and pip compatibility.

#107 TDMedina closed 4 years ago
0
Remove old flowcharts, update documentation

#106 MatthieuBeukers closed 4 years ago
0
Updated docs.

#105 pneerincx closed 4 years ago
0
Documentation updates 11-06-2020 and on

#104 MatthieuBeukers closed 4 years ago
0
Documentation 08-06-2020 update

#103 MatthieuBeukers closed 4 years ago
0
Switched to ReadTheDocs theme for MkDocs.

#102 pneerincx closed 4 years ago
0
Fix mistake in new readme.

#101 TDMedina closed 4 years ago
0
Updated documentation.

#100 pneerincx closed 4 years ago
1
New Readme

#99 TDMedina closed 4 years ago
0
Typo in help menu for --seed argument default

#98 TDMedina closed 4 years ago
1
Add first version of some documentation files

#97 MatthieuBeukers closed 4 years ago
0
WIP to master in preperation for new release.

#96 pneerincx closed 4 years ago
0
Change pip to python -m pip

#95 TDMedina closed 4 years ago
1
Latest updates to WIP branch.

#94 TDMedina closed 4 years ago
0
Add filter list (e.g. MVL) fields to VCF output INFO field

#93 TDMedina opened 4 years ago
0
Argument parsing overhaul with related changes for expanded functionality.

#92 TDMedina closed 4 years ago
0
Change logging outputs

#91 TDMedina closed 4 years ago
0
Identify sample sex for sex chromosome variants from genotype ploidy.

#90 TDMedina opened 4 years ago
0
BAM header merging broken in D-mode bam output

#89 TDMedina closed 4 years ago
0
Index_out doesn't work

#88 TDMedina closed 4 years ago
0
Check for BAM indexes in paramchecker

#87 TDMedina closed 4 years ago
0
Lynting, Refactoring, and Bug Fixes

#86 TDMedina closed 4 years ago
0
Output FASTQ donor reads from BAM are all forward direction.

#85 TDMedina closed 4 years ago
0
D-mode BAM output and other updates/changes

#84 MatthieuBeukers closed 4 years ago
0
Implementation of new 'Sample' data object and ID hashing.

#83 TDMedina closed 4 years ago
0
Variant filtering is wonky.

#82 TDMedina closed 4 years ago
0
Added utils.

#81 TDMedina closed 4 years ago
0
Implement usage of pysam.VariantRecord

#80 MatthieuBeukers closed 4 years ago
2
Hierarchical tree for selecting variants to include into a set.

#79 TDMedina opened 5 years ago
0
Consider grouping variants from the same gene from the same sample.

#78 TDMedina opened 5 years ago
1
Fix F-mode, add write config file when cli parameters are used

#77 MatthieuBeukers closed 4 years ago
0
Parallel FastQ writing in AC mode.

#76 TDMedina closed 4 years ago
0
Parallelized FastQ writing.

#75 TDMedina closed 5 years ago
0
Output config file when command line parameters are used

#74 MatthieuBeukers closed 4 years ago
1
Merge working Beta branch into Master for new release.

#73 TDMedina closed 5 years ago
0
Utils: Use variant context file to subset VCF/BCF

#72 MatthieuBeukers closed 4 years ago
2
Implement filter based on specified column and value for variant filter list (mvl)

#71 MatthieuBeukers closed 4 years ago
2
Output fixes, AC-mode semi random read distribution

#70 MatthieuBeukers closed 5 years ago
0
Fix missing FastQ mates and hardclipped reads.

#69 TDMedina closed 5 years ago
0
Samples not included in an MVL filter list are not skipped.

#68 TDMedina closed 5 years ago
1
Unmapped mate not added to P-mode FQ output.

#67 TDMedina closed 5 years ago
1
Missing newlines and,data in debug files

#66 TDMedina closed 5 years ago
1
BVCS bug in overlapping contexts

#65 TDMedina closed 4 years ago
1