htsjdk.samtools.example

Class PrintReadsExample

java.lang.Object

htsjdk.samtools.example.PrintReadsExample

public final class PrintReadsExample
extends java.lang.Object

This is a example program showing how to use SAM readers and (optionally) writers. It's also useful for measuring time. An example invocation is: java -cp dist/htsjdk-2.1.1.jar htsjdk.samtools.example.PrintReadsExample in.bam false a.bam

or (to test the IntelDeflator) java -Dsamjdk.intel_deflater_so_path=$PWD/lib/jni/libIntelDeflater.so -cp dist/htsjdk-2.1.1.jar htsjdk.samtools.example.PrintReadsExample in.bam false a.bam

Arguments: - the first argument is the input file (SAM or BAM) - the second argument is a boolean (true or false) that indicates whether reads are to be eagerly decoded (useful for benchmarking) - the third argument is optional and is the name of the output file (nothing gets written if this argument is missing)

Method Summary

Modifier and Type	Method and Description
static void	main(java.lang.String[] args)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

main

public static void main(java.lang.String[] args)
                 throws java.io.IOException

Throws:

java.io.IOException