Package htsjdk.samtools.example

Class ExampleSamUsage

java.lang.Object

htsjdk.samtools.example.ExampleSamUsage

public class ExampleSamUsage
extends Object

Constructor Summary

Constructors

Constructor	Description
ExampleSamUsage()

Method Summary

Modifier and Type	Method	Description
void	convertReadNamesToUpperCase(File inputSamOrBamFile, 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 Details

ExampleSamUsage

public ExampleSamUsage()

Method Details

myIndexSeekableStream

public static SeekableStream myIndexSeekableStream()

openSamExamples

public void openSamExamples()
                     throws MalformedURLException

Example usages of SamReaderFactory

Throws:

MalformedURLException

convertReadNamesToUpperCase

public void convertReadNamesToUpperCase(File inputSamOrBamFile,
 File outputSamOrBamFile)
                                 throws IOException

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

Throws:

IOException