From 1da7c420adbbf56fbc8efe5cd77338145f3717eb Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Wed, 5 Aug 2026 13:06:57 -0400 Subject: [PATCH 1/3] Prefix HSSS result IDs with Variant_ instead of NGS_SNP. Paired with the separator fix in ApiCommonWebService, this makes the HSSS plugins emit VariationRecordClass source_ids. This is an ApiCommon cohort default and so applies to every project in the cohort, which is safe because no project has a live snp or chip search -- those imports are commented out in the shared apiCommonModel.xml. The chip default (highspeedchipsnpsearchconfig_idPrefix: 'NULL') is left alone; the chip path is equally dead but out of scope. Co-Authored-By: Claude Opus 5 --- Model/lib/conifer/roles/conifer/vars/ApiCommon/default.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Model/lib/conifer/roles/conifer/vars/ApiCommon/default.yml b/Model/lib/conifer/roles/conifer/vars/ApiCommon/default.yml index 546e96ba5..18c9a0067 100644 --- a/Model/lib/conifer/roles/conifer/vars/ApiCommon/default.yml +++ b/Model/lib/conifer/roles/conifer/vars/ApiCommon/default.yml @@ -99,7 +99,7 @@ blastconfig_tempBlastPath: /var/www/Common/tmp/blast motifsearchconfig_motifCntxtLen: 20 highspeedsnpsearchconfig_jobsDir: /var/www/Common/tmp/highSpeedSnpSearch -highspeedsnpsearchconfig_idPrefix: NGS_SNP. +highspeedsnpsearchconfig_idPrefix: Variant_ highspeedchipsnpsearchconfig_jobsDir: /var/www/Common/tmp/highSpeedChipSnpSearch highspeedchipsnpsearchconfig_idPrefix: 'NULL' From a039aeee98e5e4138b908088aa87de38e9e3d8e2 Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Sat, 8 Aug 2026 01:23:22 -0400 Subject: [PATCH 2/3] News: corrected density and dN/dS in the sample-set SNV search Both values change for every gene, so saved strategies filtering on either will return different results. Also notes the three columns relabelled to match what they actually contain. The date attribute is left as a placeholder - it must be set to the release date before this ships. Co-Authored-By: Claude Opus 5 --- Model/lib/xml/PlasmoDB/news.xml | 37 +++++++++++++++++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/Model/lib/xml/PlasmoDB/news.xml b/Model/lib/xml/PlasmoDB/news.xml index 2b0e4b034..f23836b5b 100644 --- a/Model/lib/xml/PlasmoDB/news.xml +++ b/Model/lib/xml/PlasmoDB/news.xml @@ -31,6 +31,43 @@ --> + + Corrected statistics in the sample-set SNV search + TBD - set to the release date + + release + + +
    +
  • The SNV Characteristics Within a Group of Samples search (formerly + "SNP Characteristics") now reports SNVs per kb of coding sequence. It + previously reported all variants per kb of genomic span while labelling the + column as CDS. The previous value is still available, in a new + "SNVs per kb (gene span)" column.
    • + +
  • Its nonsynonymous/synonymous ratio is now normalized by the number of + synonymous and nonsynonymous sites in the gene, derived from the genetic code, + and is reported as dN/dS (site-normalized). The previous raw count ratio + carried the genome's codon bias: in P. falciparum the pooled + synonymous-site fraction is 17.49% rather than the textbook ~25%. Median dN/dS + across the genome moves from about 2.0 to 0.47, which is the expected + purifying-selection signature.
    • + +
  • Both values change for every gene, and saved strategies that filter on + either will return different results than they did before.
    • + +
  • Several result columns were also relabelled to match what they contain: + "Nonsynonymous SNPs" is now Missense SNVs (it never included stop-gained + variants, which are counted separately), and "Non-coding SNPs" is now + Unclassified SNVs (it covers positions where no protein product could be + assigned, not only positions outside coding sequence).
    • +
+ + ]]> + + + PlasmoDB 46 Released 6 Nov 2019 13:00 From 965009fdd47af90ab010fa91bbfda3d9523ff5f4 Mon Sep 17 00:00:00 2001 From: John Brestelli Date: Mon, 10 Aug 2026 18:27:58 -0400 Subject: [PATCH 3/3] Revert "News: corrected density and dN/dS in the sample-set SNV search" This reverts commit a039aeee98e5e4138b908088aa87de38e9e3d8e2. --- Model/lib/xml/PlasmoDB/news.xml | 37 --------------------------------- 1 file changed, 37 deletions(-) diff --git a/Model/lib/xml/PlasmoDB/news.xml b/Model/lib/xml/PlasmoDB/news.xml index f23836b5b..2b0e4b034 100644 --- a/Model/lib/xml/PlasmoDB/news.xml +++ b/Model/lib/xml/PlasmoDB/news.xml @@ -31,43 +31,6 @@ --> - - Corrected statistics in the sample-set SNV search - TBD - set to the release date - - release - - -
    -
  • The SNV Characteristics Within a Group of Samples search (formerly - "SNP Characteristics") now reports SNVs per kb of coding sequence. It - previously reported all variants per kb of genomic span while labelling the - column as CDS. The previous value is still available, in a new - "SNVs per kb (gene span)" column.
    • - -
  • Its nonsynonymous/synonymous ratio is now normalized by the number of - synonymous and nonsynonymous sites in the gene, derived from the genetic code, - and is reported as dN/dS (site-normalized). The previous raw count ratio - carried the genome's codon bias: in P. falciparum the pooled - synonymous-site fraction is 17.49% rather than the textbook ~25%. Median dN/dS - across the genome moves from about 2.0 to 0.47, which is the expected - purifying-selection signature.
    • - -
  • Both values change for every gene, and saved strategies that filter on - either will return different results than they did before.
    • - -
  • Several result columns were also relabelled to match what they contain: - "Nonsynonymous SNPs" is now Missense SNVs (it never included stop-gained - variants, which are counted separately), and "Non-coding SNPs" is now - Unclassified SNVs (it covers positions where no protein product could be - assigned, not only positions outside coding sequence).
    • -
- - ]]> - - - PlasmoDB 46 Released 6 Nov 2019 13:00