Rapid HTS Application Development using javascript and HTSJDK

Since Java SE 8, the Java JDK is shipped with a java-based javascript engine called Oracle Nashorn.

Using the Nashorn engine 'jjs' ( https://docs.oracle.com/javase/8/docs/technotes/tools/unix/jjs.html ) command-line tool and the htsjdk library it's possible to quickly develop a scripted HTS application using the htsjdk classes.

Example

Working with VCF files

The following javascript program converts a VCF file to a BED file.

if(arguments.length!=1)
	{
	java.lang.System.err.println("arguments required : one VCF File ");
	java.lang.System.exit(-1);
	}
//get stdout
var out = java.lang.System.out;
// retrieve java class for java.io.File
var File = Java.type("java.io.File");
// retrieve java class for VCFFileReader
var VCFFileReader = Java.type("htsjdk.variant.vcf.VCFFileReader");
// create a new File object
var vcfFile = new File(arguments[0]);
// open the VCF reader
var vcfFileReader = new VCFFileReader(vcfFile,false);
// get an iterator over the variants
var iter = vcfFileReader.iterator();
// print each variant as a BED file
while(iter.hasNext()) {
	var vc = iter.next();
	out.print(vc.getContig());
	out.print("\t");
	out.print( new java.lang.Integer(vc.getStart()-1));/* prevent floating number */
	out.print("\t");
	out.print(vc.getEnd());
	out.println();
	}
//cleanup
iter.close();
vcfFileReader.close();

Invocation:

jjs -cp `find htsjdk/ -name "*.jar" |tr "\n" ":"` script.js -- input.vcf

Working with BAM files

The following javascript program count the number of records in a set of BAM files:

var out=java.lang.System.out;
var File = Java.type("java.io.File");
var SamReaderFactory = Java.type("htsjdk.samtools.SamReaderFactory");

for(var idx in arguments)
	{
	var n=0;
	var samReader =  SamReaderFactory.makeDefault().open(new File(arguments[idx]));
	var iter=samReader.iterator();
		while(iter.hasNext()) {
		var rec=iter.next();
		n++;
		}

	samReader.close();
	out.println(arguments[idx]+"\t"+n);
	}

invocation:

jjs -cp `find dist build/libs -name "*.jar"  | tr "\n" ":"` script.js -- in1.bam in2.sam