From dc52d825731e65009351e1eff75ba564b1fcb878 Mon Sep 17 00:00:00 2001 From: Stephen Kazakoff Date: Wed, 15 Jan 2020 14:37:13 +1000 Subject: [PATCH 1/6] Ensure multiple queries are comma-separated --- Jasix/QueryProcessor.cs | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Jasix/QueryProcessor.cs b/Jasix/QueryProcessor.cs index 084824b5..f21ef956 100644 --- a/Jasix/QueryProcessor.cs +++ b/Jasix/QueryProcessor.cs @@ -71,7 +71,7 @@ public int ProcessQuery(IEnumerable queryStrings, bool printHeader = fal query.Chromosome = _jasixIndex.GetIndexChromName(query.Chromosome); if (!_jasixIndex.ContainsChr(query.Chromosome)) continue; - count = PrintLargeVariantsExtendingIntoQuery(query); + count += PrintLargeVariantsExtendingIntoQuery(query); count += PrintAllVariantsFromQueryBegin(query, count > 0); } From 2777e317b0c7fb46c8de9b7019d5a17b11ed5d4c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Michael=20Str=C3=B6mberg?= Date: Sat, 23 May 2020 08:00:26 -0700 Subject: [PATCH 2/6] Set theme jekyll-theme-slate --- _config.yml | 1 + 1 file changed, 1 insertion(+) create mode 100644 _config.yml diff --git a/_config.yml b/_config.yml new file mode 100644 index 00000000..c7418817 --- /dev/null +++ b/_config.yml @@ -0,0 +1 @@ +theme: jekyll-theme-slate \ No newline at end of file From b73e8ae83a86356360f2caac501f4aa290395831 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Michael=20Str=C3=B6mberg?= Date: Tue, 2 Jun 2020 18:58:56 -0700 Subject: [PATCH 3/6] Delete _config.yml --- _config.yml | 1 - 1 file changed, 1 deletion(-) delete mode 100644 _config.yml diff --git a/_config.yml b/_config.yml deleted file mode 100644 index c7418817..00000000 --- a/_config.yml +++ /dev/null @@ -1 +0,0 @@ -theme: jekyll-theme-slate \ No newline at end of file From 18c99a342c07fc6468a781a9aa3a9b2e9856b114 Mon Sep 17 00:00:00 2001 From: Michael Stromberg Date: Wed, 29 Jul 2020 11:09:54 -0700 Subject: [PATCH 4/6] Updated the version --- CommonAssemblyInfo.props | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) mode change 100644 => 100755 CommonAssemblyInfo.props diff --git a/CommonAssemblyInfo.props b/CommonAssemblyInfo.props old mode 100644 new mode 100755 index d34b835f..0aceb0f0 --- a/CommonAssemblyInfo.props +++ b/CommonAssemblyInfo.props @@ -2,9 +2,9 @@ Illumina © 2020 Illumina, Inc. - 3.9.3 - 3.9.3 - 3.9.3 + 3.10.1 + 3.10.1 + 3.10.1 Stromberg, Roy, Lajugie, Jiang, Li, and Kang From d31dd129f69bd67123bbaf42d5c5588db663821c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Michael=20Str=C3=B6mberg?= Date: Thu, 5 Nov 2020 00:07:48 -0800 Subject: [PATCH 5/6] Deprecated the wiki in favor of the GitHub Pages site --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index f2fed477..d57dbf97 100644 --- a/README.md +++ b/README.md @@ -12,6 +12,5 @@ Backronym: **NI**mble and **R**obust **VA**riant a**N**not**A**tor ## Resources -* [Getting Started](https://github.com/Illumina/Nirvana/wiki/Getting-Started) -* [Wiki](https://github.com/Illumina/Nirvana/wiki) +* [Documentation](https://illumina.github.io/NirvanaDocumentation/) * [Release Notes](https://github.com/Illumina/Nirvana/releases) From 94e527c4b7ca7f6b9865151c16effbbb64b8ce28 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Michael=20Str=C3=B6mberg?= Date: Thu, 5 Nov 2020 09:47:19 -0800 Subject: [PATCH 6/6] Update README.md --- README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/README.md b/README.md index d57dbf97..220d61aa 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,4 @@ - -
+# Nirvana Nirvana provides **clinical-grade annotation of genomic variants** (SNVs, MNVs, insertions, deletions, indels, and SVs (including CNVs). It can be run as a stand-alone package or integrated into larger software tools that require variant annotation.