iqbal-lab-org gramtools issues

iqbal-lab-org / gramtools

Genome inference from a population reference graph

MIT License

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issues

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How to use Gramtools build based on multiple VCF files?

#172 cvn001 opened 10 months ago
1
Update htslib to 1.16

#171 martinghunt closed 1 year ago
0
Update htslib

#170 martinghunt closed 1 year ago
0
make[1]: *** [CMakeFiles/Makefile2:260: libgramtools/CMakeFiles/gram.dir/rule] Error 2 make: *** [Makefile:186: gram] Error 2

#169 joybio closed 1 year ago
6
gramtools gramtools backend expected at: /home/tools/anaconda3/lib/python3.7/site-packages/gramtools/bin/gram but not found

#168 kdyoung100 closed 1 year ago
2
install error

#167 8banzhuan opened 1 year ago
1
gramtools build error

#166 duzezhen closed 1 year ago
1
Error while running gramtools

#165 khodor14 opened 2 years ago
2
Migrate to pyproject.toml

#164 bricoletc closed 2 years ago
0
Ubuntu 18.04 install woes

#163 kdm9 closed 2 years ago
3
Stop installing py-cortex-api by default

#162 bricoletc closed 2 years ago
0
Install error

#161 shehongbing closed 1 year ago
3
Unable to run the geamtools discover command successfully

#160 duzezhen closed 2 years ago
4
Retire variant-aware kmer indexing code

#159 bricoletc closed 1 year ago
0
Boost download link is dead, breaks gramtools compilation process

#158 bricoletc closed 3 years ago
4
Error Installing gramtools

#157 mezewudo closed 3 years ago
8
'N' in reference genome fasta not supported

#156 bricoletc opened 3 years ago
0
Release 1.7

#155 bricoletc closed 3 years ago
1
Release 1.6.0

#154 bricoletc closed 4 years ago
5
Handle no variants after clustering

#153 martinghunt closed 4 years ago
8
Pf benchmarking

#152 bricoletc opened 4 years ago
1
Per base coverage recording error

#151 bricoletc closed 4 years ago
0
Cortex dependency on stampy

#150 bricoletc closed 3 years ago
3
Proper concurrent querying of alleles

#149 bricoletc closed 4 years ago
9
Better first time construction of PRG string from VCF

#148 bricoletc closed 4 years ago
5
Encoding chromosome boundaries in PRG string

#147 bricoletc closed 4 years ago
0
Performance cost of kmer-indexing

#146 iqbal-lab opened 5 years ago
1
Reducing index size

#145 bricoletc opened 5 years ago
1
Multi-threading improvements

#144 bricoletc opened 5 years ago
4
Vcf rebasing in `discover` is not exhaustive

#143 bricoletc closed 5 years ago
0
Why the cache?

#142 bricoletc closed 5 years ago
5
`left_markers_search` instruction bottleneck

#141 bricoletc closed 5 years ago
2
Fix #139: Correct allele ID found even when PRG alphabet is discontinuous

#140 ffranr closed 5 years ago
1
Kmer index unit test assigns an allele ID of zero to search state

#139 ffranr closed 5 years ago
3
Kmer indexing code refactoring

#138 bricoletc closed 5 years ago
0
Simplify site marker boundary discovery

#137 bricoletc closed 4 years ago
0
Missing sample column from infer output

#136 iqbal-lab closed 5 years ago
5
Install issue into a python venv

#135 nzmacalasdair closed 5 years ago
2
Discover command

#134 ffranr closed 5 years ago
4
exit from gramtools build with non-zero exit code

#133 iqbal-lab closed 6 years ago
4
Benchmarking TB: build and quasimap

#132 ffranr closed 4 years ago
3
Minimum 1 layer deep nesting to support long deletions

#131 ffranr closed 4 years ago
1
Build PRG from MSA and more sparsely from VCF

#130 ffranr opened 6 years ago
4
Memory issue in current tip of gramtools?

#129 iqbal-lab closed 6 years ago
7
Release 0.6 criteria

#128 iqbal-lab closed 4 years ago
6
Quasimapping with multiple threads odd behaviour

#127 iqbal-lab closed 5 years ago
15
Clarify quasimap reported read count

#126 iqbal-lab closed 6 years ago
2
Benchmarking basic MHC (8haplos): build and quasimap

#125 iqbal-lab opened 6 years ago
0
We may need kmer indexing for higher k to enable acceptable quasimapping

#124 iqbal-lab closed 6 years ago
2
Remove skip optimisation code

#123 ffranr closed 6 years ago
1