https://github.com/bigdatagenomics/convert

Conversions to and from Big Data Genomics Avro Formats. Apache 2 licensed.
https://github.com/bigdatagenomics/convert

Last synced: about 2 months ago
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Conversions to and from Big Data Genomics Avro Formats. Apache 2 licensed.

• Host: GitHub
• URL: https://github.com/bigdatagenomics/convert
• Owner: bigdatagenomics
• License: apache-2.0
• Created: 2016-09-16T17:03:08.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2022-12-02T15:43:09.000Z (about 2 years ago)
• Last Synced: 2024-05-02T00:29:18.207Z (8 months ago)
• Language: Java
• Homepage:
• Size: 213 KB
• Stars: 0
• Watchers: 5
• Forks: 5
• Open Issues: 2
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGES.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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README

        
# convert

[![Maven Central](https://img.shields.io/maven-central/v/org.bdgenomics.convert/convert.svg?maxAge=600)](http://search.maven.org/#search%7Cga%7C1%7Corg.bdgenomics.convert)

[![API Documentation](http://javadoc.io/badge/org.bdgenomics.convert/convert.svg?color=brightgreen&label=javadoc)](http://javadoc.io/doc/org.bdgenomics.convert/convert)

### Hacking convert

Install

 * JDK 1.8 or later, http://openjdk.java.net

 * Apache Maven 3.8.5 or later, http://maven.apache.org

To build

    $ mvn install

### About convert

The [`Converter`](https://github.com/bigdatagenomics/convert/blob/master/convert/src/main/java/org/bdgenomics/convert/Converter.java)

interface, inspired by Apache [Commons Convert](https://commons.apache.org/sandbox/commons-convert/)

(sandbox component, never released), provides for converting from a source type `S` to a target type `T`, with a

[conversion stringency](https://github.com/bigdatagenomics/convert/blob/master/convert/src/main/java/org/bdgenomics/convert/ConversionStringency.java)

and [SLF4J logger](http://www.slf4j.org/) given as context.

```java

public interface Converter {

  T convert(S source, ConversionStringency stringency, Logger logger) throws ConversionException;

  // ...

}

```

Rather than implement a custom converter registry, `convert` relies on dependency injection via Google [Guice](https://github.com/google/guice).

Use the `@Inject` annotation to inject converters into class constructors:

```java

final class MyClass {

  private final Converter ontologyTermConverter) {

    this.ontologyTermConverter = ontologyTermConverter;

  }

  void doIt() {

    OntologyTerm ontologyTerm = ontologyTermConverter.convert("SO:0000110", stringency, logger);

  }

}

```

The Guice injector handles construction of the converter instances, managing nested converter dependencies

as necessary (if say, a `Gff3Record` to `Feature` converter depends on a `String` to `Strand` converter).

Some converters may require late bindings; for those a converter factory is available via injection:

```java

final class MyClass {

  private final AlignmentRecordToSamRecordFactory alignmentRecordToSamRecordFactory;

  private final ConversionStringency stringency = ConversionStringency.STRICT;

  private static final logger = LoggerFactory.getLogger(MyClass.class);

  @Inject

  MyClass(final AlignmentRecordToSamRecordFactory alignmentRecordToSamRecordFactory) {

    this.alignmentRecordToSamRecordFactory = alignmentRecordToSamRecordFactory;

  }

  void doIt() {

    AlignmentRecord alignmentRecord = ...;

    SAMFileHeader header = ...;

    Converter converter = alignmentRecordToSamRecordFactory.create(header);

    SAMRecord record = converter.convert(alignmentRecord, stringency, logger);

  }

}

```