Use Squirls as a library

Squirls has been designed to be used as a library within a larger frameworks for prioritization of genome variants. This document explains how to use Squirls API classes to enable including splicing deleteriousness predictions into a Java software.

The following sections describe how to use Squirls as a module in other Java tool.

Install Squirls modules into your local Maven repository

Please run the following command to install Squirls into the local Maven repository:

git checkout https://github.com/TheJacksonLaboratory/Squirls
cd Squirls
./mvnw install

Note

The installation requires JDK11+ to be present on the platform

Spring Boot application

After the successful installation, add the following dependency into your pom.xml to use Squirls in a Spring boot app:

<dependency>
  <groupId>org.monarchinitiative.squirls</groupId>
  <artifactId>squirls-spring-boot-starter</artifactId>
  <version>1.0.0</version>
</dependency>

After adding the dependency, Spring configures VariantSplicingEvaluator bean, provided that the environment properties

• squirls.data-directory

• squirls.genome-assembly

• squirls.data-version

are set to proper values.

The VariantSplicingEvaluator provides the following methods to calculate SquirlsResult for a Variant specified by Svart library:

SquirlsResult evaluate(Variant variant, Set<String> txIds);
SquirlsResult evaluate(Variant variant);

Please see the corresponding Javadocs to learn more about VariantSplicingEvaluator, SquirlsResult, etc.