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
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)