Static Public Member Functions
static Sequence	getChrSequence (String seqDir, String chr) throws IOException

static String	getChrSizesFile (String seqDir)

static ContinuousDataAlignmentModel	getDataModel (String bamFile, String sizeFile, String chr, boolean removeDuplicates) throws IOException

static ContinuousDataAlignmentModel	getDataModel (String bamFile, String sizeFile, boolean removeDuplicates) throws IOException

static ContinuousDataAlignmentModel	getDataModel (String bamFile, String sizeFile, int minMappingQuality, boolean removeDuplicateFlags, boolean weighReadCounts, String strand, boolean loadPairsAsFragments) throws IOException

Member Function Documentation

static Sequence broad.core.sequence.SequenceUtils.getChrSequence	(	String	seqDir,
		String	chr
	)		throws IOException

static

static String broad.core.sequence.SequenceUtils.getChrSizesFile ( String seqDir )

static

static ContinuousDataAlignmentModel broad.core.sequence.SequenceUtils.getDataModel	(	String	bamFile,
		String	sizeFile,
		String	chr,
		boolean	removeDuplicates
	)		throws IOException

static

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static ContinuousDataAlignmentModel broad.core.sequence.SequenceUtils.getDataModel	(	String	bamFile,
		String	sizeFile,
		boolean	removeDuplicates
	)		throws IOException

static

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static ContinuousDataAlignmentModel broad.core.sequence.SequenceUtils.getDataModel	(	String	bamFile,
		String	sizeFile,
		int	minMappingQuality,
		boolean	removeDuplicateFlags,
		boolean	weighReadCounts,
		String	strand,
		boolean	loadPairsAsFragments
	)		throws IOException

static

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

Static Public Member Functions