fix(archaic): keep strict-mask sites marked so the HG002 Neanderthal share lands within the published range by geiresx · Pull Request #52 · geiresx/OwnGenome

fix(sv): judge a Delly RDCN on chrX and chrY by the sample's sex and the PARs

GeiserX

committed

eca3fc1

fix(sv): stop step 05 on an SV VCF with more than one sample

GeiserX

committed

bcc082e

fix(recheck): see image digest changes, skip opt-in steps the run left out, never crash on a bad header

GeiserX

committed

6f40667

build(renovate): track the nf-weblog plugin pin of the live site

GeiserX

committed

ae61a34

fix(sv): pass a large integral RDCN to the depth rule as digits

GeiserX

committed

feb1f11

ci(e2e): keep the table builders' downloads in the data cache, mirror first

GeiserX

committed

bc9dede

test(e2e): fail a case that ran no check

GeiserX

committed

04122f8

ci(e2e): run the cases when .github/actions changes, and refuse globs outside the scope

GeiserX

committed

b61283b

test(e2e): run step 53 and setup.sh --locityper-data on the fixture

GeiserX

committed

f921e9f

ci(sv): give build-sv-rule-regions.sh a --check mode, a cache and --list

GeiserX

committed

a0924d2

docs(testing): the catalogs data entry, the no-check rule, the scope check and the Locityper case

GeiserX

committed

9ba3195

Merge remote-tracking branch 'origin/main' into pgp/ci-e2e

GeiserX

committed

3f2d011

fix(sv): let only a PASS, non-reference Manta call hide a Delly or CNVpytor call

GeiserX

committed

a154ca7

fix(recheck): leave out the pins of opt-in steps a default run never planned

GeiserX

committed

acf47c9

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fix(archaic): keep strict-mask sites marked so the HG002 Neanderthal share lands within the published range - #52

fix(archaic): keep strict-mask sites marked so the HG002 Neanderthal share lands within the published range#52
geiresx wants to merge 27 commits into
mainfrom
pgp/archaic-2

Commits on Nov 6, 2026

fix(sv): judge a Delly RDCN on chrX and chrY by the sample's sex and the PARs

fix(sv): stop step 05 on an SV VCF with more than one sample

fix(recheck): see image digest changes, skip opt-in steps the run left out, never crash on a bad header

build(renovate): track the nf-weblog plugin pin of the live site

fix(sv): pass a large integral RDCN to the depth rule as digits

ci(e2e): keep the table builders' downloads in the data cache, mirror first

test(e2e): fail a case that ran no check

ci(e2e): run the cases when .github/actions changes, and refuse globs outside the scope

test(e2e): run step 53 and setup.sh --locityper-data on the fixture

ci(sv): give build-sv-rule-regions.sh a --check mode, a cache and --list

docs(testing): the catalogs data entry, the no-check rule, the scope check and the Locityper case

Merge remote-tracking branch 'origin/main' into pgp/ci-e2e

fix(sv): let only a PASS, non-reference Manta call hide a Delly or CNVpytor call

fix(recheck): leave out the pins of opt-in steps a default run never planned

Commits on Nov 7, 2026

test(e2e): keep the Locityper case to HLA-DQB1, well inside its time limit

fix(sv): keep a Delly 0/0 or ./. call out of AnnotSV's input

test(e2e): give the Locityper case 90 minutes, since jellyfish alone takes 35

test(archaic): fail a chr22 Neanderthal share over the published 95th percentile

fix(archaic): mark the rows outside the strict mask instead of dropping them

docs(archaic): say the strict mask now marks rows and what the chr22 gate is

ci(e2e): the Locityper case's measured time, and review fixes to the catalog builders

test(archaic): guard the chr22 share at 1,200 kb and set the kept-row floor from the measured run

test(archaic): make the e2e header say what the chr22 gate is

train: #314 on main and the PRs queued before it

train: #311 on main and the PRs queued before it

train: #322 on main and the PRs queued before it

train: #323 on main and the PRs queued before it