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alimanfoo
/
vcfnp
Load numpy arrays and HDF5 files from VCF (variant call format)
MIT License
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vcfnp.variants abbreviates strings in CHROM column
#65
alexhbnr
closed
7 years ago
3
number of files doesn't match
#64
xiekunwhy
closed
8 years ago
3
genotype_ac
#63
alimanfoo
closed
8 years ago
0
EFF Amino_Acid_Change field being truncated
#62
travc
closed
8 years ago
2
Flatten EFF/ANN annotations?
#61
alimanfoo
closed
8 years ago
1
is_snp fix
#60
podpearson
closed
8 years ago
1
Compress files created by vcf2npy
#59
alimanfoo
closed
8 years ago
0
bugfix for vcf2hdf5_parallel
#58
travc
closed
8 years ago
5
vcfnpy2hdf5 increase default chunk size to 1Mb
#57
alimanfoo
closed
8 years ago
1
Region fix (resolves alimanfoo/vcnfp#54)
#56
travc
closed
8 years ago
4
resolve for #54
#55
travc
closed
9 years ago
0
bug generating hdf5 from vcf
#54
travc
closed
8 years ago
1
use shutil.which to get vcf2npy and vcfnpy2hdf5
#53
travc
closed
8 years ago
1
messed up vcf2hdf5_parallel pull request
#52
travc
closed
9 years ago
1
Initial vcf2hdf5_parallel
#51
travc
closed
9 years ago
2
full vcf to hdf5...
#50
travc
closed
9 years ago
3
git clone error
#49
travc
closed
9 years ago
3
Convert C++ exceptions into Python exceptions
#48
kyleabeauchamp
closed
8 years ago
11
Remove version logging from scripts
#47
alimanfoo
closed
9 years ago
0
Remove numpy build dependency
#46
alimanfoo
closed
8 years ago
0
Added explicit numpy header include to setup.py
#45
kyleabeauchamp
closed
9 years ago
3
Removing -h flag
#44
hardingnj
closed
9 years ago
1
Support PY3
#43
alimanfoo
closed
9 years ago
0
Add option to only pack calldata
#42
benjeffery
closed
9 years ago
4
Genotype packed
#41
alimanfoo
closed
9 years ago
1
Local parallelisation for vcf2npy
#40
alimanfoo
closed
9 years ago
1
vcfnp2hdf5 add vcf header definitions as attributes on datasets
#39
alimanfoo
opened
10 years ago
0
vcfnp2hdf5 less verbose logging on load
#38
alimanfoo
closed
9 years ago
0
vcfnpy2blz
#37
alimanfoo
closed
8 years ago
1
vcfnpy2hdf5 add chunk width option
#36
alimanfoo
closed
10 years ago
0
Change samples to dataset
#35
alimanfoo
closed
10 years ago
0
Fix calldata fields such that all dimensions are included in shape
#34
alimanfoo
closed
10 years ago
0
Reorganise variants as group with child dataset per field
#33
alimanfoo
closed
10 years ago
0
Missing genotype but non-missing calldata
#32
alimanfoo
closed
10 years ago
0
qsub_vcf2npy breaks for -tc or any similar qsub option
#31
alimanfoo
opened
10 years ago
0
flatten EFF field in vcf2csv
#30
alimanfoo
closed
10 years ago
0
EFF defaults
#29
alimanfoo
closed
10 years ago
0
fix command line script incorrect use of nargs
#28
alimanfoo
closed
10 years ago
0
fix bug for string fields with multiple values
#27
alimanfoo
closed
10 years ago
1
script for converting VCF to CSV
#26
alimanfoo
closed
10 years ago
2
script for loading hdf5
#25
alimanfoo
closed
10 years ago
0
scripts for parallelizing conversion to npy
#24
alimanfoo
closed
10 years ago
0
log last variant position with progress
#23
alimanfoo
opened
10 years ago
0
add more default INFO dtypes
#22
alimanfoo
closed
10 years ago
0
user-specified cachedir
#21
alimanfoo
closed
10 years ago
0
auto cache
#20
alimanfoo
closed
10 years ago
0
calldata_2d
#19
alimanfoo
closed
10 years ago
0
combine info() and variants()
#18
alimanfoo
closed
11 years ago
1
flatten FILTER
#17
alimanfoo
closed
11 years ago
1
variants() throws ValueError reporting two fields with the same name?
#16
alimanfoo
closed
11 years ago
1
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