bio_relatives

Program, which determines the relationship between people at the level of mother / father / child.

Table of Contents

• Requirements
• Installing
• Building
  • Creation of the project in IntelliJ
• Running integration tests
• Usage
  • Options
  • Examples
    • Comparison of the genomes of two persons
    • Comparison of the genomes of three persons
    • Comparison of the genomes with intermediate output
• Maintainers
• Contributing
• License

Requirements

• To run bio_relatives project:
  • Java 8 JDK or higher
• To build bio_relatives project:
  • Java 8 JDK or higher
  • Git 2.5 or higher
  • Gradle 3.1 or higher. We recommend using the ./gradlew script, which will download and use an appropriate gradle version automatically (see examples below).

Installing

You can download the latest version of the project from github releases page.

Building

bio_relatives project can be built using gradle.

A wrapper script ./gradlew will download the appropriate version of the gradle on the first invocation.

Examples of gradle usage from the bio_relatives root directory:

• compile and build a jar

./gradlew

or

./gradlew jar

The jar file will be in build/libs/bio_relatives-\<version\>.jar. Version is based on the current git commit.

• run tests

./gradlew test

• clean project directory

./gradlew clean

• build a jar file that includes all of bio_relatives's dependencies

./gradlew shadowJar

• create a snapshot and install it into your local maven repository

./gradlew install

• for an exhaustive list of all available targets

./gradlew tasks

Creation of the project using IntelliJ

To create the project in IntelliJ IDE for bio_relatives do the following:

1. Select fom the menu: File -> New -> Project from Existing Sources
2. In the resulting dialog, chose Import from existing model, select Gradle and Next
3. Choose the default gradle wrapper and Finish.

Running integration tests

To run the integration tests, go to the src/test/bash/. If you need to test Levenshtein comparison, then run the script levenstein_comparison_test.sh the usual way(the script does not require any arguments): ./levenshtein_comparison_test.sh. If you need to test STR comparison, then run the script str_comparison_test.sh with argument X(for X-STR comparison) or Y(for Y-STR comparison). For example, ./str_comparison_test Y. The output of each test can be found in the src/test/bash/output/ folder. You can see the expected test results in the src/test/bash/expected/ folder. You can see the difference between the test and expected data in the src/test/bash/output

Usage

java -jar bio_relatives.jar [-h | --help] [-io | --intermediateOutput] [-g | --graph <path to the file>] [-c2 | --compare2 <first> <second> <bed>] [-c3 | --compare3 <father> <mother> <son> <bed>] [-m | --mode <L | XY>] [-th | --threadsNumber <number>]

Options

-h, --help - show help message.

-io, --intermediateOutput - key, which enables intermediate results output.

-c2, --compare2 - compare genomes of two persons.

-c3, --compare3 - compare genomes of three persons (father/mother/son).

-m, --mode - defines which comparator will be used.

-g, --graph - defines whether graph should be printed or not (used only in STR comparison).

-th, --threadsNumber - defines number of threads that should be created to process the information analysis.

Examples

Comparison of the genomes of two persons

java -jar bio_relatives.jar --compare2 ~/path/to/first.bam ~/path/to/second.bam ~/path/to/file.bed

Comparison of the genomes of three persons

java -jar bio_relatives.jar --compare3 ~/path/to/father.bam ~/path/to/mother.bam ~/path/to/son.bam ~/path/to/file.bed

Comparison of the genomes with intermediate output

java -jar bio_relatives.jar -io -c2 ~/path/to/first.bam ~/path/to/second.bam ~/path/to/file.bed

Maintainers

• Polina Bevad
• Sergey Hvatov
• Vladislav Marchenko

Contributing

Please read Contributing.md for more details about our code of conduct, and the process of submitting pull requests to us.

License

This project is licenced under the terms of the MIT license.