org.utgenome.format.sam
Class Sam2WigConverter.CoverageWriter

java.lang.Object
  extended by 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


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