broad.pda.seq.alignment.AlignmentUtils Class Reference

Collaboration diagram for broad.pda.seq.alignment.AlignmentUtils:

Static Public Member Functions
static void	main (String[] args) throws Exception
static ContinuousDataAlignmentModel	loadAlignmentData (String alignmentFile) throws IOException
static ContinuousDataAlignmentModel	loadAlignmentData (String alignmentFile, boolean loadChromosomeStats) throws IOException
static ContinuousDataAlignmentModel	loadAlignmentData (String alignmentFile, boolean loadChromosomeStats, int minMappingQuality) throws IOException
static ContinuousDataAlignmentModel	loadAlignmentData (String alignmentFile, boolean loadChromosomeStats, int minMappingQuality, boolean removeDuplicateFlags) throws IOException
static ContinuousDataAlignmentModel	loadAlignmentData (String alignmentFile, boolean loadChromosomeStats, boolean removeDuplicateFlags, boolean weighReadCounts) throws IOException
static ContinuousDataAlignmentModel	loadAlignmentData (String alignmentFile, boolean loadChromosomeStats, int minMappingQuality, boolean removeDuplicateFlags, boolean weighReadCounts) throws IOException
static ContinuousDataAlignmentModel	loadAlignmentData (String alignmentFile, boolean loadChromosomeStats, int minMappingQuality, boolean removeDuplicateFlags, boolean weighReadCounts, String strand) throws IOException
static ContinuousDataAlignmentModel	loadAlignmentData (String alignmentFile, boolean loadChromosomeStats, int minMappingQuality, boolean removeDuplicateFlags, boolean weighReadCounts, String strand, boolean loadPairsAsFragments) throws IOException
static void	scoreAnnotations (BEDReader annotationReader, ContinuousDataAlignmentModel data) throws IOException
static Map< String, Integer >	getSizesFromSAM (String samFileName)
static Gene	SAMFormatFullBED (SAMRecord sam)

Member Function Documentation

static Map<String, Integer> broad.pda.seq.alignment.AlignmentUtils.getSizesFromSAM ( String  samFileName )

static

static ContinuousDataAlignmentModel broad.pda.seq.alignment.AlignmentUtils.loadAlignmentData ( String  alignmentFile ) throws IOException

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static ContinuousDataAlignmentModel broad.pda.seq.alignment.AlignmentUtils.loadAlignmentData ( String  alignmentFile, boolean  loadChromosomeStats  ) throws IOException

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static ContinuousDataAlignmentModel broad.pda.seq.alignment.AlignmentUtils.loadAlignmentData ( String  alignmentFile, boolean  loadChromosomeStats, int  minMappingQuality  ) throws IOException

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static ContinuousDataAlignmentModel broad.pda.seq.alignment.AlignmentUtils.loadAlignmentData ( String  alignmentFile, boolean  loadChromosomeStats, int  minMappingQuality, boolean  removeDuplicateFlags  ) throws IOException

static

Author

: skadri

Parameters

alignmentFile	Name of alignment file
loadChromosomeStats	File with chromosome stats
minMappingQuality	Mapping quality threshold
removeDuplicateFlags	Set to true if PCR duplicates should be ignored

Returns

Exceptions

IOException

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static ContinuousDataAlignmentModel broad.pda.seq.alignment.AlignmentUtils.loadAlignmentData ( String  alignmentFile, boolean  loadChromosomeStats, boolean  removeDuplicateFlags, boolean  weighReadCounts  ) throws IOException

static

Author

: skadri

Parameters

alignmentFile	Name of alignment file
loadChromosomeStats	File with chromosome stats
removeDuplicateFlags	Set to true if PCR duplicates should be ignored
weighReadCounts	Set to true if read counts will be weighed by the NH flag

Returns

Exceptions

IOException

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static ContinuousDataAlignmentModel broad.pda.seq.alignment.AlignmentUtils.loadAlignmentData ( String  alignmentFile, boolean  loadChromosomeStats, int  minMappingQuality, boolean  removeDuplicateFlags, boolean  weighReadCounts  ) throws IOException

static

Author

: skadri

Parameters

alignmentFile	Name of alignment file
loadChromosomeStats	File with chromosome stats
minMappingQuality	Mapping quality threshold = will be set to 0.0 if weighReadCounts is true
removeDuplicateFlags	Set to true if PCR duplicates should be ignored
weighReadCounts	Set to true if read counts will be weighed by the NH flag

Returns

Exceptions

IOException

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static ContinuousDataAlignmentModel broad.pda.seq.alignment.AlignmentUtils.loadAlignmentData ( String  alignmentFile, boolean  loadChromosomeStats, int  minMappingQuality, boolean  removeDuplicateFlags, boolean  weighReadCounts, String  strand  ) throws IOException

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static ContinuousDataAlignmentModel broad.pda.seq.alignment.AlignmentUtils.loadAlignmentData ( String  alignmentFile, boolean  loadChromosomeStats, int  minMappingQuality, boolean  removeDuplicateFlags, boolean  weighReadCounts, String  strand, boolean  loadPairsAsFragments  ) throws IOException

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static void broad.pda.seq.alignment.AlignmentUtils.main ( String[]  args ) throws Exception

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static Gene broad.pda.seq.alignment.AlignmentUtils.SAMFormatFullBED ( SAMRecord  sam )

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static void broad.pda.seq.alignment.AlignmentUtils.scoreAnnotations ( BEDReader  annotationReader, ContinuousDataAlignmentModel  data  ) throws IOException

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

• java/broad/pda/seq/alignment/AlignmentUtils.java