org.utgenome.format.sam
Class Sam2WigConverter

java.lang.Object
  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