org.utgenome.format.sam
Class Sam2WigConverter.CoverageWriter

java.lang.Object
  org.utgenome.format.sam.Sam2WigConverter.CoverageWriter

All Implemented Interfaces:

ReadDepth.DepthOutput

Enclosing class:

Sam2WigConverter

public static class Sam2WigConverter.CoverageWriter
extends Object
implements ReadDepth.DepthOutput

Constructor Summary

Sam2WigConverter.CoverageWriter(Writer out)

Method Summary

void	flush()
void	outputHeader(String chr, int start)
void	reportDepth(String chr, int start, int end, int depth)
void	switchChr()

Methods inherited from class java.lang.Object

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

Constructor Detail

Sam2WigConverter.CoverageWriter

public Sam2WigConverter.CoverageWriter(Writer out)
                                throws IOException

Throws:

IOException

Method Detail

switchChr

public void switchChr()

outputHeader

public void outputHeader(String chr,
                         int start)
                  throws IOException

Throws:

IOException

flush

public void flush()
           throws IOException

Throws:

IOException

reportDepth

public void reportDepth(String chr,
                        int start,
                        int end,
                        int depth)
                 throws IOException

Specified by:

reportDepth in interface ReadDepth.DepthOutput

Throws:

IOException