Package htsjdk.samtools.example
Class ExampleSamUsage
- java.lang.Object
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- htsjdk.samtools.example.ExampleSamUsage
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public class ExampleSamUsage extends Object
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Constructor Summary
Constructors Constructor Description ExampleSamUsage()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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 ofSamReaderFactory
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Method Detail
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myIndexSeekableStream
public static SeekableStream myIndexSeekableStream()
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openSamExamples
public void openSamExamples() throws MalformedURLException
Example usages ofSamReaderFactory
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MalformedURLException
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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
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