org.utgenome.format.sam
Class Sam2WigConverter

java.lang.Object
  extended by org.utgenome.format.sam.Sam2WigConverter

public class Sam2WigConverter
extends Object

Converting SAM into WIG (coverage depth)

Author:
leo

Nested Class Summary
static class Sam2WigConverter.CoverageWriter
           
static class Sam2WigConverter.SAMRecordCursor
          Iterator of SAMRecord
 
Constructor Summary
Sam2WigConverter()
           
 
Method Summary
 void convert(File samOrBam, String chr, int start, int end)
           
 void convert(File samOrBam, Writer out)
          Convert the input SAM file records into WIG format of read depth
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Sam2WigConverter

public Sam2WigConverter()
Method Detail

convert

public void convert(File samOrBam,
                    Writer out)
             throws UTGBException
Convert the input SAM file records into WIG format of read depth

Parameters:
samOrBam -
out -
Throws:
IOException
UTGBException

convert

public void convert(File samOrBam,
                    String chr,
                    int start,
                    int end)
             throws UTGBException
Throws:
UTGBException


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