From 84bf0db63320170fa05c12f5354f08124cb70a5b Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Mon, 15 Nov 2021 16:57:06 +0100 Subject: [PATCH 1/5] Fix DAB1 pathologic unit name --- stranger/resources/variant_catalog_hg19.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/stranger/resources/variant_catalog_hg19.json b/stranger/resources/variant_catalog_hg19.json index 4a20ebe..3d89b23 100755 --- a/stranger/resources/variant_catalog_hg19.json +++ b/stranger/resources/variant_catalog_hg19.json @@ -370,7 +370,7 @@ ], "VariantId": [ "DAB1_ATTTT1", - "DAB1_ATTTC", + "DAB1", "DAB1_ATTTT2" ], "PathologicRegion": "chr1:57832725-57832780", From 086ed5585dd9b9f1a66ff63717e0b524c76f1849 Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Mon, 15 Nov 2021 16:58:08 +0100 Subject: [PATCH 2/5] Fix #42 - changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0e9a3a5..5b64cb8 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,7 @@ All notable changes to this project will be documented in this file. This project adheres to [Semantic Versioning](http://semver.org/). ## [x.x.x] +Fix DAB1 pathologic repeat unit name ## [0.8.0] Off by one error on PathogenticMin output. All affected have at least been cautioned pre_mutation with proper size. From 9fa365228ce8ed1d6c1cad1d0ea9d17ff48741ac Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Mon, 15 Nov 2021 18:06:12 +0100 Subject: [PATCH 3/5] Update POLG coords --- stranger/resources/variant_catalog_grch37.json | 8 ++++---- stranger/resources/variant_catalog_grch38.json | 8 ++++---- stranger/resources/variant_catalog_hg19.json | 6 +++--- stranger/resources/variant_catalog_hg38.json | 8 ++++---- 4 files changed, 15 insertions(+), 15 deletions(-) diff --git a/stranger/resources/variant_catalog_grch37.json b/stranger/resources/variant_catalog_grch37.json index 16b4e50..0ff2989 100755 --- a/stranger/resources/variant_catalog_grch37.json +++ b/stranger/resources/variant_catalog_grch37.json @@ -370,7 +370,7 @@ ], "VariantId": [ "DAB1_ATTTT1", - "DAB1_ATTTC", + "DAB1", "DAB1_ATTTT2" ], "PathologicRegion": "1:57832725-57832780", @@ -1008,10 +1008,10 @@ "LocusStructure": "(CTG)*TTG(CTG)*", "VariantType": ["Repeat","Repeat"], "VariantId": ["POLG_I", "POLG_II"], - "ReferenceRegion": ["15:89876820-89876826", - "15:89876829-89876859"], + "ReferenceRegion": ["15:89876821-89876826", + "15:89876830-89876859"], "NormalMax": 15, "PathologicMin": 10000, - "PathologicRegion": "15:89876829-89876859" + "PathologicRegion": "15:89876830-89876859" } ] diff --git a/stranger/resources/variant_catalog_grch38.json b/stranger/resources/variant_catalog_grch38.json index 536c0c7..3df4ac2 100644 --- a/stranger/resources/variant_catalog_grch38.json +++ b/stranger/resources/variant_catalog_grch38.json @@ -389,7 +389,7 @@ ], "VariantId": [ "DAB1_ATTTT1", - "DAB1_ATTTC", + "DAB1", "DAB1_ATTTT2" ], "PathologicRegion": "1:57367053-57367108", @@ -1217,10 +1217,10 @@ "SourceId": "CMMS", "VariantId": ["POLG_I", "POLG_II"], "LocusStructure": "(CTG)*TTG(CTG)*", - "ReferenceRegion": ["15:89833580-89833586", - "15:89833589-89833628"], + "ReferenceRegion": ["15:89333590-89333595", + "15:89333599-89333628"], "NormalMax": 15, "PathologicMin": 10000, - "PathologicRegion": "15:89833589-89833628" + "PathologicRegion": "15:89333599-89333628" } ] diff --git a/stranger/resources/variant_catalog_hg19.json b/stranger/resources/variant_catalog_hg19.json index 3d89b23..5b6f77d 100755 --- a/stranger/resources/variant_catalog_hg19.json +++ b/stranger/resources/variant_catalog_hg19.json @@ -1008,10 +1008,10 @@ "LocusStructure": "(CTG)*TTG(CTG)*", "VariantType": ["Repeat","Repeat"], "VariantId": ["POLG_I", "POLG_II"], - "ReferenceRegion": ["chr15:89876820-89876826", - "chr15:89876829-89876859"], + "ReferenceRegion": ["chr15:89876821-89876826", + "chr15:89876830-89876859"], "NormalMax": 15, "PathologicMin": 10000, - "PathologicRegion": "chr15:89876829-89876859" + "PathologicRegion": "chr15:89876830-89876859" } ] diff --git a/stranger/resources/variant_catalog_hg38.json b/stranger/resources/variant_catalog_hg38.json index 4c05404..da43798 100644 --- a/stranger/resources/variant_catalog_hg38.json +++ b/stranger/resources/variant_catalog_hg38.json @@ -389,7 +389,7 @@ ], "VariantId": [ "DAB1_ATTTT1", - "DAB1_ATTTC", + "DAB1", "DAB1_ATTTT2" ], "PathologicRegion": "chr1:57367053-57367108", @@ -1217,10 +1217,10 @@ "SourceId": "CMMS", "VariantId": ["POLG_I", "POLG_II"], "LocusStructure": "(CTG)*TTG(CTG)*", - "ReferenceRegion": ["chr15:89833580-89833586", - "chr15:89833589-89833628"], + "ReferenceRegion": ["chr15:89333590-89333595", + "chr15:89333599-89333628"], "NormalMax": 15, "PathologicMin": 10000, - "PathologicRegion": "chr15:89833589-89833628" + "PathologicRegion": "chr15:89333599-89333628" } ] From ffe40059e0890b2f517cd82430ee8658af1d9164 Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Mon, 15 Nov 2021 18:09:26 +0100 Subject: [PATCH 4/5] Fix #41 - POLG hg38 - but also hg19 --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 5b64cb8..3c23c28 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,7 @@ This project adheres to [Semantic Versioning](http://semver.org/). ## [x.x.x] Fix DAB1 pathologic repeat unit name +Update POLG coords, quite a bit on hg38 ## [0.8.0] Off by one error on PathogenticMin output. All affected have at least been cautioned pre_mutation with proper size. From 84c9760a265e66cf0c9a577e154ea5e3d941ae24 Mon Sep 17 00:00:00 2001 From: Daniel Nilsson Date: Mon, 15 Nov 2021 18:12:37 +0100 Subject: [PATCH 5/5] Bump version to v0.8.1 --- CHANGELOG.md | 2 ++ stranger/__version__.py | 2 +- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 3c23c28..80fc052 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,8 @@ All notable changes to this project will be documented in this file. This project adheres to [Semantic Versioning](http://semver.org/). ## [x.x.x] + +## [0.8.1] Fix DAB1 pathologic repeat unit name Update POLG coords, quite a bit on hg38 diff --git a/stranger/__version__.py b/stranger/__version__.py index 32a90a3..ef72cc0 100644 --- a/stranger/__version__.py +++ b/stranger/__version__.py @@ -1 +1 @@ -__version__ = '0.8.0' +__version__ = '0.8.1'