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vgteam
/
toil-vg
Distributed and cloud computing framework for vg
Apache License 2.0
21
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14
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update sveval image
#793
glennhickey
closed
4 years ago
0
Allow Giraffe to exist in paired-end conditions in mapeval
#792
adamnovak
closed
4 years ago
0
Python 3
#791
glennhickey
closed
4 years ago
2
fix typo where gam_chunking option gets forgotten
#790
glennhickey
closed
4 years ago
0
Fix calling with augmenting but no gam chunking
#789
glennhickey
closed
4 years ago
0
update vg docker
#788
glennhickey
closed
4 years ago
0
Small fixes
#787
glennhickey
closed
4 years ago
0
Account for vg producing multiple types of HandleGraphs
#786
adamnovak
closed
4 years ago
7
update vg docker image
#785
glennhickey
closed
4 years ago
0
Revise chunking options for toil-vg call
#784
glennhickey
closed
4 years ago
0
[WIP] Add a new disk ensurer that is easier to call and use it for GAM merging
#783
adamnovak
opened
4 years ago
0
Allow passing options like k and w to vg minimizer
#782
adamnovak
closed
4 years ago
0
WIP: Rewrite toil-vg call
#781
glennhickey
closed
4 years ago
0
Remove the right directory when someone else has downloaded a tool
#780
adamnovak
closed
4 years ago
0
Kubernetes patches
#779
adamnovak
closed
4 years ago
0
Make --force_phasing also ignore overlaps
#778
adamnovak
closed
4 years ago
0
--force_phasing True on toil-vg construct doesn't work
#777
adamnovak
opened
4 years ago
2
Skip minimizer without gbwt
#776
adamnovak
closed
4 years ago
1
Make sure we don't forget about chr22 when rewriting contig names
#775
adamnovak
closed
4 years ago
0
Using --add_chr_prefix gives me `22` instead of `chr22`
#774
adamnovak
closed
4 years ago
2
Flat requirements for whole genome mode are wasteful
#773
adamnovak
opened
4 years ago
0
Phasing VCF argument validation fixes, and Kubernetes compatibility patches
#772
adamnovak
closed
4 years ago
0
Fix docs for --filter_samples
#771
adamnovak
closed
4 years ago
0
Smooth out calling options
#770
glennhickey
closed
4 years ago
0
use vg paths instead of mod to abide by new interface
#769
glennhickey
closed
4 years ago
0
Default to Singularity if it works and Docker doesn't
#768
adamnovak
closed
4 years ago
0
Option to include alt paths in xg index
#767
glennhickey
closed
4 years ago
0
update vg docker image version
#766
glennhickey
closed
5 years ago
0
toil-vg call has a "no_augment" option, but does not appear to perform the "vg augment" step by default
#765
briannadon
closed
5 years ago
3
Fix CI
#764
glennhickey
closed
5 years ago
0
Support new version of vg call
#763
glennhickey
closed
5 years ago
0
move back to development release
#762
glennhickey
closed
5 years ago
0
update default vg docker image
#761
glennhickey
closed
5 years ago
0
toil-vg call error[vg chunk]: input path somepathname not found in xg index
#760
alancleary
closed
4 years ago
8
toil-vg call throws XGFormatError: Unimplemented XG format version: 0
#759
alancleary
opened
5 years ago
4
Add Giraffe Support
#758
adamnovak
closed
5 years ago
0
fix chunk options
#757
glennhickey
closed
5 years ago
1
Pack support for toil-vg call
#756
glennhickey
closed
5 years ago
0
switch to toil 3.20
#755
glennhickey
closed
5 years ago
5
Simplify calling interface
#754
glennhickey
closed
4 years ago
0
Update SV calling opts
#753
glennhickey
closed
5 years ago
0
update vg docker
#752
glennhickey
closed
5 years ago
0
Add test for SV genotyping
#751
glennhickey
closed
5 years ago
0
Update vg docker
#750
glennhickey
closed
5 years ago
0
GBWT changes broke haplotype extraction
#749
glennhickey
closed
5 years ago
3
Fix alt-path indexing
#748
glennhickey
closed
5 years ago
0
update default vg docker image version
#747
glennhickey
closed
5 years ago
0
bump up toil version in make prepare
#746
glennhickey
closed
5 years ago
0
Tests for toil-vg call --genotype_vcf
#745
glennhickey
closed
5 years ago
1
Report read file line mismatches
#744
adamnovak
closed
4 years ago
1
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