broad.core.sequence.TranscribedSequenceComposition Class Reference

Collaboration diagram for broad.core.sequence.TranscribedSequenceComposition:

Public Member Functions
	TranscribedSequenceComposition (String bamFile, String geneBedFile, String genomeFasta, TranscriptionRead transcriptionRead) throws IOException
	TranscribedSequenceComposition (String bamFile, String geneBedFile, String bedFileRegionsOfInterest, String genomeFasta, TranscriptionRead transcriptionRead) throws IOException
char	getTranscribedBaseAtBeginningPosition (Gene parent, Alignment read, int offset) throws IOException

Static Public Member Functions
static void	main (String[] args) throws IOException

Protected Attributes
Collection< String >	allNucleotides

Detailed Description

Author

prussell

Constructor & Destructor Documentation

broad.core.sequence.TranscribedSequenceComposition.TranscribedSequenceComposition	(	String	bamFile,
		String	geneBedFile,
		String	genomeFasta,
		TranscriptionRead	transcriptionRead
	)		throws IOException

Parameters

bamFile	Bam file
geneBedFile	Bed file of genes
genomeFasta	Genome fasta file
transcriptionRead	Transcription read

Exceptions

IOException

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broad.core.sequence.TranscribedSequenceComposition.TranscribedSequenceComposition	(	String	bamFile,
		String	geneBedFile,
		String	bedFileRegionsOfInterest,
		String	genomeFasta,
		TranscriptionRead	transcriptionRead
	)		throws IOException

Parameters

bamFile	Bam file
geneBedFile	Bed file of genes
bedFileRegionsOfInterest	Bed file of regions within genes
genomeFasta	Genome fasta file
transcriptionRead	Transcription read

Exceptions

IOException

Member Function Documentation

char broad.core.sequence.TranscribedSequenceComposition.getTranscribedBaseAtBeginningPosition	(	Gene	parent,
		Alignment	read,
		int	offset
	)		throws IOException

Get transcribed base of parent gene at first position of alignment

Parameters

parent	Parent gene
read	Alignment
offset	Offset along the parent transcript from the beginning position

Returns

The transcribed base or N if read orientation does not match parent gene strand

Exceptions

IOException

static void broad.core.sequence.TranscribedSequenceComposition.main ( String[]  args ) throws IOException

static

Parameters

args

Exceptions

IOException

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Member Data Documentation

Collection<String> broad.core.sequence.TranscribedSequenceComposition.allNucleotides

protected

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The documentation for this class was generated from the following file:

• java/broad/core/sequence/TranscribedSequenceComposition.java