Overview

This is a strict streaming parser for VCF 4.1/4.2.

The main parser class (VcfParser) is responsible for reading all metadata and initial position data. Then actual handling of each position line is delegated to an implementation of VcfLineParser.

Check out VcfParserTest.java for a quick and dirty view of it in action.

MemoryMappedVcfLineParser is a implementation of VcfLineParser that reads everything into memory.

Get It

Maven

<dependencies>
  ...
  <dependency>
    <groupId>org.pharmgkb</groupId>
    <artifactId>vcf-parser</artifactId>
    <version>0.3.1</version>
  </dependency>
  ...
</dependencies>

Non-Maven

You can download jars from the Central Maven Repository.