v0.3.0 #29

smlmbrt · 2022-10-21T11:08:00Z

No description provided.

Split matching and aggregate logs to create scoring files

…ncluded matches (e.g. variant-double counting). Previously it would have been considering across mutliple scores.

…ide the extension(s)

…sing the file name instead of the PGS ID

Create logs for combine_scorefiles

… |-bar demimited headers reappear

Fix to separate traits

Collect minimum information when writing out scorefiles

smlmbrt · 2022-11-21T11:03:20Z

I think the utils are now ready for v0.3 and coupling too v1.3 in pgsc_calc

nebfield and others added 13 commits October 18, 2022 15:39

split matches by chromosome and aggregate them

026c07f

bump version

ed7d700

fix summary log

dc748ff

fix types

a0b6072

add aggregate_matches

66b1b8a

fix summary log aggregation

67c13c0

fix tests and rename -> combine_matches

b22a008

fix invalid pgs id

c7011c7

keep match_variants functionality (optional)

eafd0fb

fix tests

4a60897

clarify log message

a1c1ffb

check for duplicate IDs in matches before writing scoring files

abb5fd9

Merge pull request #28 from PGScatalog/aggregate_matches

7b16581

Split matching and aggregate logs to create scoring files

smlmbrt linked an issue Oct 21, 2022 that may be closed by this pull request

Further match_variants optimisations #27

Closed

smlmbrt and others added 16 commits October 21, 2022 13:39

Handle descendant EFO terms to be excluded from trait queries

2c7216e

Update assertion to make sure the same ID isn't present in multiple i…

dbae744

…ncluded matches (e.g. variant-double counting). Previously it would have been considering across mutliple scores.

Fixed missing max statement

50868f5

lazy write

01e0718

fix test with extreme prejudice

5a202b5

Fix typo

452f76c

Fix basename function when a file name contains 'dot' characters outs…

4944e7d

…ide the extension(s)

Generate a combined log file containing score headers information

758a843

Add more Harmonization logs and liftover logs. Change the log ID by u…

721e3ec

…sing the file name instead of the PGS ID

improve build cache and add build argument

8001210

collect lazy matches just before writing

5b8b8ec

update dependencies

d932b4d

be extremely lazy

32edf28

Better log message

343a799

don't .fetch()

fc6e604

Merge remote-tracking branch 'origin/dev' into dev

960927e

smlmbrt and others added 9 commits November 10, 2022 14:37

Simplify label error parsing

c01aafc

Merge pull request #30 from ens-lgil/feature/combine_logs

4ee6237

Create logs for combine_scorefiles

Fix output and naming convention for logfile

182715f

fix scorefile output + add test to check format

0fabd9c

Log: extract pgp_id and fix ',' in reported trait bug. TODO: fix when…

8b7f696

… |-bar demimited headers reappear

Fix to separate traits

6edcc11

Merge pull request #32 from ens-lgil/hotfix/combine_logs

c215e4a

Fix to separate traits

Use correct delimited for mapped/efo traits

67f0f67

Add variant number to log for custom scoring files

774af6f

nebfield marked this pull request as ready for review November 11, 2022 17:31

smlmbrt linked an issue Nov 13, 2022 that may be closed by this pull request

Adapt combine_scorefiles to output information from scoring file headers #24

Closed

8 tasks

nebfield and others added 11 commits November 14, 2022 12:56

check if --outdir exists

6174e85

just check if <--outdir>/matches exists -_-

8d101f9

move tempdir

ceb27ec

stop chatty logs re: mmap

a93a32f

fix tempdir with combine_matches

785684f

fix workdir

eeb0681

fix match_variants not respecting --outdir

a8481a3

be slightly less lazy

0b1de5a

Collect matches by chromosome to reduce RAM?

86aac22

collect minimal columns for writing only

4761906

Merge pull request #33 from PGScatalog/opt_chrom

9741d51

Collect minimum information when writing out scorefiles

smlmbrt requested a review from nebfield November 21, 2022 11:02

nebfield approved these changes Nov 21, 2022

View reviewed changes

smlmbrt added 2 commits November 21, 2022 11:51

Write full log as csv

c43e85d

Merge remote-tracking branch 'origin/dev' into opt_chrom

01a92ac

nebfield approved these changes Nov 21, 2022

View reviewed changes

nebfield merged commit e220f14 into main Nov 21, 2022

nebfield deleted the dev branch November 21, 2022 12:52

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v0.3.0 #29

v0.3.0 #29

smlmbrt commented Oct 21, 2022

smlmbrt commented Nov 21, 2022

v0.3.0 #29

v0.3.0 #29

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smlmbrt commented Oct 21, 2022

smlmbrt commented Nov 21, 2022