htsjdk.samtools.example

Class ExampleSamUsage

java.lang.Object

htsjdk.samtools.example.ExampleSamUsage

public class ExampleSamUsage
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
ExampleSamUsage()

Method Summary

Modifier and Type	Method and Description
void	convertReadNamesToUpperCase(java.io.File inputSamOrBamFile, java.io.File outputSamOrBamFile) Read a SAM or BAM file, convert each read name to upper case, and write a new SAM or BAM file.
static SeekableStream	myIndexSeekableStream()
void	openSamExamples() Example usages of SamReaderFactory

Methods inherited from class java.lang.Object

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

Constructor Detail

ExampleSamUsage

public ExampleSamUsage()

Method Detail

myIndexSeekableStream

public static SeekableStream myIndexSeekableStream()

openSamExamples

public void openSamExamples()
                     throws java.net.MalformedURLException

Example usages of SamReaderFactory

Throws:

java.net.MalformedURLException

convertReadNamesToUpperCase

public void convertReadNamesToUpperCase(java.io.File inputSamOrBamFile,
                                        java.io.File outputSamOrBamFile)
                                 throws java.io.IOException

Read a SAM or BAM file, convert each read name to upper case, and write a new SAM or BAM file.

Throws:

java.io.IOException