Merge pull request #246

Update URLs after the repository move

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
 

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

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 <https://github.com/TheJacksonLaboratory/SvAnna/releases>`_.
+Download and extract SvAnna distribution ZIP archive from `here <https://github.com/monarch-initiative/SvAnna/releases>`_.
 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 <https://github.com/TheJacksonLaboratory/SvAnna/blob/master/svanna-cli/src/examples/example.vcf>`_::
+First, let's download the VCF file from `here <https://github.com/monarch-initiative/SvAnna/blob/master/svanna-cli/src/examples/example.vcf>`_::
 
-  $ 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.
 

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
+.. _example.vcf: https://github.com/monarch-initiative/SvAnna/blob/master/svanna-cli/src/examples/example.vcf

docs/setup.rst

@@ -21,7 +21,7 @@ Prebuilt SvAnna executable
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 To download the executable SvAnna JAR file, go to the
-`Releases section <https://github.com/TheJacksonLaboratory/SvAnna/releases>`_
+`Releases section <https://github.com/monarch-initiative/SvAnna/releases>`_
 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
 

docs/tutorial.rst

@@ -30,7 +30,7 @@ If you have a VCF file on hand that was called with a caller such as `pbsv <http
 `sniffles <https://github.com/fritzsedlazeck/Sniffles>`_, or `SVIM <https://github.com/eldariont/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 <https://github.com/TheJacksonLaboratory/SvAnna/blob/master/svanna-cli/src/examples/example.vcf>`_.
+The file with the 8 variants can be downloaded here: `svanna-cli/src/examples/example.vcf <https://github.com/monarch-initiative/SvAnna/blob/master/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 <https://phenopacket-schema.readthedocs.io/en/latest/basics.html>`_ 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 <https://github.com/TheJacksonLaboratory/PhenopacketGenerator>`_ for
+be done in a text editor but we recommend the `PhenopacketGenerator <https://github.com/monarch-initiative/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 <https://github.com/TheJacksonLaboratory/SvAnna/blob/master/svanna-cli/src/examples/example-phenopacket.json>`_.
+This phenopacket file can be downloaded here: `svanna-cli/src/examples/example-phenopacket.json <https://github.com/monarch-initiative/SvAnna/blob/master/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 <https://github.com/TheJacksonLaboratory/SvAnna/issues>`_.
+And that's it! If you encounter any problems, please create an issue on the SvAnna `tracker <https://github.com/monarch-initiative/SvAnna/issues>`_.

pom.xml

@@ -62,9 +62,9 @@
     </developers>
 
     <scm>
-        <connection>scm:git:git@github.com:TheJacksonLaboratory/SvAnna.git</connection>
-        <developerConnection>scm:git:git@github.com:TheJacksonLaboratory/SvAnna.git</developerConnection>
-        <url>scm:git:git@github.com:TheJacksonLaboratory/SvAnna.git</url>
+        <connection>scm:git:git@github.com:monarch-initiative/SvAnna.git</connection>
+        <developerConnection>scm:git:git@github.com:monarch-initiative/SvAnna.git</developerConnection>
+        <url>scm:git:git@github.com:monarch-initiative/SvAnna.git</url>
         <tag>v${project.version}</tag>
     </scm>
 

svanna-cli/src/main/resources/org/monarchinitiative/svanna/cli/writer/html/template/svannHTML.ftl

@@ -526,7 +526,7 @@ a.svg:hover, a.svg:active {
   <footer>
       <div style="text-align: center">
           <p>Developed by <em>Daniel Danis</em> and <em>Peter N Robinson</em> at <a href="https://www.jax.org">The Jackson Laboratory for Genomic Medicine</a>.</p>
-          <p>Problems, suggestions, or comments? Feel free to submit an issue to our <a href="https://github.com/TheJacksonLaboratory/SvAnna/issues">GitHub tracker</a>.</p>
+          <p>Problems, suggestions, or comments? Feel free to submit an issue to our <a href="https://github.com/monarch-initiative/SvAnna/issues">GitHub tracker</a>.</p>
           <p>&#169; 2022 Daniel Danis, Peter N Robinson</p>
       </div>
   </footer>

svanna-io/src/test/java/org/monarchinitiative/svanna/io/parse/VcfVariantParserTest.java

@@ -425,7 +425,7 @@ public void toVariants_breakendVariant() {
     }
 
     /**
-     * Per issue <a href="https://github.com/TheJacksonLaboratory/SvAnna/issues/235">235</a>,
+     * Per issue <a href="https://github.com/monarch-initiative/SvAnna/issues/235">235</a>,
      * HTSlib &gt;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}.
      * <p>