org.utgenome.util
Class ReadDepth

java.lang.Object
  org.utgenome.util.ReadDepth

public class ReadDepth
extends Object

Read depth computation in O(2N) time.

Author:

leo

Nested Class Summary

static interface

ReadDepth.DepthOutput

Constructor Summary

protected

ReadDepth(ReadDepth.DepthOutput out)

Method Summary

static void	compute(String chr, Iterator<GenomeRange> cursor, ReadDepth.DepthOutput out) Compute the read depth of the input read set.
protected void	computeDepth(String chr, Iterator<GenomeRange> cursor)

Methods inherited from class java.lang.Object

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

Constructor Detail

ReadDepth

protected ReadDepth(ReadDepth.DepthOutput out)

Method Detail

compute

public static void compute(String chr,
                           Iterator<GenomeRange> cursor,
                           ReadDepth.DepthOutput out)
                    throws Exception

Compute the read depth of the input read set. The read set must be sorted by start order.

Parameters:

cursor -

out -

Throws:

Exception

computeDepth

protected void computeDepth(String chr,
                            Iterator<GenomeRange> cursor)
                     throws Exception

Throws:

Exception