diff --git a/README.md b/README.md index b2cb8884..1db43bf4 100644 --- a/README.md +++ b/README.md @@ -1,13 +1,13 @@ # SvAnna - Structural Variant Annotation and Analysis -[![GitHub release](https://img.shields.io/github/release/TheJacksonLaboratory/SvAnna.svg)](https://github.com/TheJacksonLaboratory/SvAnna/releases) -[![Java CI with Maven](https://github.com/TheJacksonLaboratory/SvAnna/workflows/Java%20CI%20with%20Maven/badge.svg)](https://github.com/TheJacksonLaboratory/SvAnna/actions/workflows/maven.yml) +[![GitHub release](https://img.shields.io/github/release/monarch-initiative/SvAnna.svg)](https://github.com/monarch-initiative/SvAnna/releases) +[![Java CI with Maven](https://github.com/monarch-initiative/SvAnna/workflows/Java%20CI%20with%20Maven/badge.svg)](https://github.com/monarch-initiative/SvAnna/actions/workflows/maven.yml) [![Documentation Status](https://readthedocs.org/projects/svanna/badge/?version=master)](https://svanna.readthedocs.io/en/master/?badge=master) Efficient and accurate pathogenicity prediction for coding and regulatory structural variants in long-read genome sequencing. Most users should download the latest SvAnna distribution ZIP file from -the [Releases page](https://github.com/TheJacksonLaboratory/SvAnna/releases). +the [Releases page](https://github.com/monarch-initiative/SvAnna/releases). ## Example use diff --git a/docs/examples.rst b/docs/examples.rst index c3ae4917..b60fc5ac 100644 --- a/docs/examples.rst +++ b/docs/examples.rst @@ -263,7 +263,7 @@ Command -.. _examples.vcf: https://github.com/TheJacksonLaboratory/SvAnna/blob/master/svanna-cli/src/examples/example.vcf +.. _examples.vcf: https://github.com/monarch-initiative/SvAnna/blob/master/svanna-cli/src/examples/example.vcf .. _Decoding NF1 Intragenic Copy-Number Variations: https://pubmed.ncbi.nlm.nih.gov/26189818 .. _The first case report of a large deletion of the BRCA1 gene in Croatia: https://pubmed.ncbi.nlm.nih.gov/29310340 .. _Whole-exome sequencing and digital PCR identified a novel compound heterozygous mutation in the NPHP1 gene in a case of Joubert syndrome and related disorders: https://pubmed.ncbi.nlm.nih.gov/28347285 @@ -272,4 +272,4 @@ Command .. _Deletion of Exon 1 in AMER1 in Osteopathia Striata with Cranial Sclerosis: https://pubmed.ncbi.nlm.nih.gov/33265914 .. _Functional characterization of a 13-bp deletion (c.-1522_-1510del13) in the promoter of the von Willebrand factor gene in type 1 von Willebrand disease: https://pubmed.ncbi.nlm.nih.gov/20696945 .. _Phenotypic consequences of gene disruption by a balanced de novo translocation involving SLC6A1 and NAA15: https://pubmed.ncbi.nlm.nih.gov/29621621 -.. _run_examples.sh: https://github.com/TheJacksonLaboratory/SvAnna/blob/development/svanna-cli/src/examples/run_examples.sh +.. _run_examples.sh: https://github.com/monarch-initiative/SvAnna/blob/development/svanna-cli/src/examples/run_examples.sh diff --git a/docs/quickstart.rst b/docs/quickstart.rst index b8edb510..76d5584e 100644 --- a/docs/quickstart.rst +++ b/docs/quickstart.rst @@ -28,7 +28,7 @@ SvAnna is installed by running the following three steps. 1. Download SvAnna distribution ZIP ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -Download and extract SvAnna distribution ZIP archive from `here `_. +Download and extract SvAnna distribution ZIP archive from `here `_. Expand the *Assets* menu and download the ``svanna-cli-${project.version}-distribution.zip``. Choose the latest stable version, or a release candidate (RC). @@ -60,9 +60,9 @@ Prioritize structural variants in VCF file ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Let's annotate a toy VCF file containing eight SVs reported in the SvAnna manuscript. -First, let's download the VCF file from `here `_:: +First, let's download the VCF file from `here `_:: - $ wget https://raw.githubusercontent.com/TheJacksonLaboratory/SvAnna/master/svanna-cli/src/examples/example.vcf + $ wget https://raw.githubusercontent.com/monarch-initiative/SvAnna/master/svanna-cli/src/examples/example.vcf The variants were sourced from published clinical case reports and presence of each variant results in a Mendelian disease. diff --git a/docs/running.rst b/docs/running.rst index d1876f46..c6880101 100644 --- a/docs/running.rst +++ b/docs/running.rst @@ -89,4 +89,4 @@ SvAnna configuration See the next section to learn more about the SvAnna :ref:`rstoutputformats`, and the :ref:`rstexamples` section to see how SvAnna prioritizes various SV classes. -.. _example.vcf: https://github.com/TheJacksonLaboratory/SvAnna/blob/master/svanna-cli/src/examples/example.vcf \ No newline at end of file +.. _example.vcf: https://github.com/monarch-initiative/SvAnna/blob/master/svanna-cli/src/examples/example.vcf \ No newline at end of file diff --git a/docs/setup.rst b/docs/setup.rst index 93d3af45..589af3f5 100644 --- a/docs/setup.rst +++ b/docs/setup.rst @@ -21,7 +21,7 @@ Prebuilt SvAnna executable ~~~~~~~~~~~~~~~~~~~~~~~~~~~ To download the executable SvAnna JAR file, go to the -`Releases section `_ +`Releases section `_ on the SvAnna GitHub page and download the latest SvAnna ZIP archive. @@ -52,7 +52,7 @@ are required for build. Run the following commands to download SvAnna source code from GitHub repository and to build SvAnna JAR file:: - $ git clone https://github.com/TheJacksonLaboratory/SvAnna + $ git clone https://github.com/monarch-initiative/SvAnna $ cd SvAnna $ ./mvnw package diff --git a/docs/tutorial.rst b/docs/tutorial.rst index 980dcd7c..997e2b8e 100644 --- a/docs/tutorial.rst +++ b/docs/tutorial.rst @@ -30,7 +30,7 @@ If you have a VCF file on hand that was called with a caller such as `pbsv `_, or `SVIM `_, it can be used instead or you can add the 8 variants to the end of that file to simulate a "real-life" long-read seuqencing experiment. -The file with the 8 variants can be downloaded here: `svanna-cli/src/examples/example.vcf `_. +The file with the 8 variants can be downloaded here: `svanna-cli/src/examples/example.vcf `_. Running SvAnna in VCF-only mode ############################### @@ -74,7 +74,7 @@ with disease, patient, and genetic information, enabling clinicians, biologists, build more complete models of disease. See the `GA4GH documentation `_ for more information. Importantly, to run SvAnna with a Phenopacket, the path of the VCF file needs to be recorded in the Phenopacket. This can -be done in a text editor but we recommend the `PhenopacketGenerator `_ for +be done in a text editor but we recommend the `PhenopacketGenerator `_ for convenience -- enter the HPO terms and the path to the VCF file. The following is a minimal Phenopacket (note this is version 1, we will add support for the v2 in near future). :: @@ -117,7 +117,7 @@ To run this on your system, replace the path for the VCF file (``file:///***/*** have the VCF file at ``/home/myname/data/example.vcf``, the line should read ``"uri": "file:///home/myname/data/example.vcf"``. -This phenopacket file can be downloaded here: `svanna-cli/src/examples/example-phenopacket.json `_. +This phenopacket file can be downloaded here: `svanna-cli/src/examples/example-phenopacket.json `_. Note however, that you will need to adjust the path to the VCF file as described just above. This command will prioritize the SVs according to phenotypic relevance. We entered a single HPO term, @@ -148,4 +148,4 @@ The deletion is visualized as follows. :width: 800 :alt: VWF deletion -And that's it! If you encounter any problems, please create an issue on the SvAnna `tracker `_. \ No newline at end of file +And that's it! If you encounter any problems, please create an issue on the SvAnna `tracker `_. \ No newline at end of file diff --git a/pom.xml b/pom.xml index 1e3aefe7..30d33876 100644 --- a/pom.xml +++ b/pom.xml @@ -62,9 +62,9 @@ - scm:git:git@github.com:TheJacksonLaboratory/SvAnna.git - scm:git:git@github.com:TheJacksonLaboratory/SvAnna.git - scm:git:git@github.com:TheJacksonLaboratory/SvAnna.git + scm:git:git@github.com:monarch-initiative/SvAnna.git + scm:git:git@github.com:monarch-initiative/SvAnna.git + scm:git:git@github.com:monarch-initiative/SvAnna.git v${project.version} diff --git a/svanna-cli/src/main/resources/org/monarchinitiative/svanna/cli/writer/html/template/svannHTML.ftl b/svanna-cli/src/main/resources/org/monarchinitiative/svanna/cli/writer/html/template/svannHTML.ftl index 37f7c2d7..8bb65f71 100644 --- a/svanna-cli/src/main/resources/org/monarchinitiative/svanna/cli/writer/html/template/svannHTML.ftl +++ b/svanna-cli/src/main/resources/org/monarchinitiative/svanna/cli/writer/html/template/svannHTML.ftl @@ -526,7 +526,7 @@ a.svg:hover, a.svg:active { diff --git a/svanna-io/src/test/java/org/monarchinitiative/svanna/io/parse/VcfVariantParserTest.java b/svanna-io/src/test/java/org/monarchinitiative/svanna/io/parse/VcfVariantParserTest.java index fc8297d6..001b2c09 100644 --- a/svanna-io/src/test/java/org/monarchinitiative/svanna/io/parse/VcfVariantParserTest.java +++ b/svanna-io/src/test/java/org/monarchinitiative/svanna/io/parse/VcfVariantParserTest.java @@ -425,7 +425,7 @@ public void toVariants_breakendVariant() { } /** - * Per issue 235, + * Per issue 235, * HTSlib >1.17 produces a gzipped file that cannot be read by common-compress's `GzipCompressorInputStream`. * As a fix, the class was replaced by JRE's {@link java.util.zip.GZIPInputStream}. *