feat(traits): print the LPA KIV-2 null allele beside the copy count and the SMN1 silent-carrier marker beside psCN by geiresx · Pull Request #327 · GeiserX/OwnGenome

fix(report): read a header-only Y tree path table as an empty path

GeiserX

committed

3a13913

fix(report): read no copy from a phased GT with an uncalled allele

GeiserX

committed

5c2776d

fix(live): pin the nf-weblog plugin in versions.env with a Renovate rule

GeiserX

committed

9f19f15

fix(report): read the CFTR and UGT1A1 repeats without overclaiming

GeiserX

committed

c7a136a

docs: say what the report search, the Nextflow report and the tests really cover

GeiserX

committed

70c0742

fix(schema): name the cram,crai and gvcf,gvcf_index samplesheet columns in --input

GeiserX

committed

7a4c99e

test(docs): fail when a schema parameter has no row in docs/parameters.md

GeiserX

committed

7d310a4

fix(report): say a homozygous R117H with no 5T copy sits on both copies

GeiserX

committed

d85e9d5

docs(report): say a chrX, chrY or chrM expansion position can be a search term

GeiserX

committed

6d8c717

feat(traits): read copy-aware markers from the reads at every GRCh38 copy of the site

GeiserX

committed

b8073df

feat(lpa): print the KIV-2 4925G>A null allele beside the KIV-2 count

GeiserX

committed

ff45aae

feat(paralogs): read the SMN1 g.27134T>G silent-carrier marker beside the SMN1 psCN

GeiserX

committed

c925be1

test(e2e): plant and clear the LPA and SMN1 markers in HG002 reads; docs and contract rows

GeiserX

committed

84a6072

test(ci): plant a flipped LPA marker and drop the 2+0 sentence, to watch the new checks go red

GeiserX

committed

daa0f55

Revert the planted flipped LPA marker and the dropped 2+0 sentence

GeiserX

committed

2ef9c14

fix(lpa): add the 4925G>A rows through traits_report.py, so step 46 calls no table layout script

GeiserX

committed

655087b

fix(lpa): keep step 46's table as it was and write the 4925G>A reading to its own file

GeiserX

committed

46149a4

fix(traits): read the markers as not assessed when their reads cannot be trusted

GeiserX

committed

07c9292

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feat(traits): print the LPA KIV-2 null allele beside the copy count and the SMN1 silent-carrier marker beside psCN - #327

feat(traits): print the LPA KIV-2 null allele beside the copy count and the SMN1 silent-carrier marker beside psCN#327
GeiserX merged 24 commits into
GeiserX:mainfrom
geiresx:pgp/genotype-rules-2

Commits on Nov 7, 2026

fix(report): read a header-only Y tree path table as an empty path

fix(report): read no copy from a phased GT with an uncalled allele

fix(live): pin the nf-weblog plugin in versions.env with a Renovate rule

fix(report): read the CFTR and UGT1A1 repeats without overclaiming

docs: say what the report search, the Nextflow report and the tests really cover

fix(schema): name the cram,crai and gvcf,gvcf_index samplesheet columns in --input

test(docs): fail when a schema parameter has no row in docs/parameters.md

fix(report): say a homozygous R117H with no 5T copy sits on both copies

docs(report): say a chrX, chrY or chrM expansion position can be a search term

feat(traits): read copy-aware markers from the reads at every GRCh38 copy of the site

feat(lpa): print the KIV-2 4925G>A null allele beside the KIV-2 count

feat(paralogs): read the SMN1 g.27134T>G silent-carrier marker beside the SMN1 psCN

test(e2e): plant and clear the LPA and SMN1 markers in HG002 reads; docs and contract rows

test(ci): plant a flipped LPA marker and drop the 2+0 sentence, to watch the new checks go red

Revert the planted flipped LPA marker and the dropped 2+0 sentence

fix(lpa): add the 4925G>A rows through traits_report.py, so step 46 calls no table layout script

fix(lpa): keep step 46's table as it was and write the 4925G>A reading to its own file

fix(traits): read the markers as not assessed when their reads cannot be trusted

Commits on Nov 8, 2026

test(e2e): select the LPA null-allele case when the LPA module changes

Merge origin/main into pgp/followups-report

docs(export): say why the round trip leaves chrM out now that chip-to-vcf moves 23andMe MT sites

Merge remote-tracking branch 'origin/main' into pgp/genotype-rules-2

train: #325 on main and the PRs queued before it

train: #327 on main and the PRs queued before it