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PGScatalog
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pgscatalog_utils
(superseded by pygscatalog) Utilities for working with PGS Catalog API and scoring files
Apache License 2.0
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Ancestry tools & reports
#38
smlmbrt
closed
1 year ago
0
Add MD5 checksum validation
#37
ens-lgil
closed
1 year ago
4
More informative error messages
#36
smlmbrt
opened
1 year ago
1
Validate downloaded scoring files with checksum
#35
nebfield
closed
1 year ago
3
Replace home-brewed batching with `read_csv_batched`
#34
nebfield
closed
2 months ago
2
Collect minimum information when writing out scorefiles
#33
nebfield
closed
1 year ago
0
Fix to separate traits
#32
ens-lgil
closed
1 year ago
0
Reimplement the output of concatenated scoring files
#31
smlmbrt
closed
1 year ago
1
Create logs for combine_scorefiles
#30
ens-lgil
closed
1 year ago
0
v0.3.0
#29
smlmbrt
closed
1 year ago
1
Split matching and aggregate logs to create scoring files
#28
nebfield
closed
1 year ago
1
Further match_variants optimisations
#27
smlmbrt
closed
1 year ago
1
`v0.2.0` release
#26
nebfield
closed
1 year ago
0
Setup a user agent for the download_scorefiles utils (REST API calls to the PGS Catalog)
#25
ens-lgil
closed
1 year ago
2
Adapt combine_scorefiles to output information from scoring file headers
#24
smlmbrt
closed
1 year ago
2
Track API statistics
#23
smlmbrt
closed
1 year ago
1
Scoring file validators tool
#22
ens-lgil
closed
1 year ago
0
Profile and reduce memory usage in `match_variants`
#21
nebfield
closed
1 year ago
2
Compress outputs
#20
nebfield
closed
1 year ago
0
Handle PGS Catalog REST API errors and retries
#19
ens-lgil
closed
1 year ago
0
Performance improvement checklist
#18
nebfield
closed
1 year ago
1
v0.1.2 release
#17
nebfield
closed
1 year ago
0
Catch ftp download errors
#16
ens-lgil
closed
1 year ago
0
API & FTP Request Error-handling
#15
smlmbrt
closed
1 year ago
0
Add summary log to combine_scorefiles
#14
nebfield
closed
1 year ago
1
Improve labelling and filtering of match candidates (e.g. duplicates)
#13
nebfield
closed
1 year ago
0
Handle genome build information
#12
smlmbrt
closed
1 year ago
1
Track/Flag duplicated variants
#11
smlmbrt
closed
1 year ago
0
Check if scoring files are in PGS Catalog format with JSON schema
#10
nebfield
closed
1 year ago
6
Merge dev for release v0.1.1
#9
nebfield
closed
2 years ago
0
Track unmatched variants in match_variants
#8
smlmbrt
closed
1 year ago
2
use matched_effect_allele
#7
nebfield
closed
2 years ago
3
Keep missing vars
#6
smlmbrt
closed
2 years ago
0
Add flag to consider/ignore strand flips
#5
smlmbrt
closed
2 years ago
1
Adapt download_scorefile to download both author-reported scoring files and harmonized files
#4
smlmbrt
closed
2 years ago
0
Fix matching
#3
smlmbrt
closed
2 years ago
0
Adapt match_variants to allow VCF files as input
#2
smlmbrt
opened
2 years ago
0
Advanced API queries
#1
smlmbrt
closed
2 years ago
1
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