ExampleSamUsage (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.example.ExampleSamUsage

public class ExampleSamUsage
extends Object

Constructor Summary

Constructors
Constructor and Description

ExampleSamUsage()

Constructors
Constructor and Description
`ExampleSamUsage()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and 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 Detail
- ExampleSamUsage
```
public ExampleSamUsage()
```

Method Detail

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

Class ExampleSamUsage

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

ExampleSamUsage

Method Detail

myIndexSeekableStream

openSamExamples

convertReadNamesToUpperCase