broad.pda.seq.alignment.StoredAlignmentStats Class Reference

Public Member Functions
	StoredAlignmentStats () throws IOException
void	load (File alignmentStoredStatFile) throws NumberFormatException, IOException
long	getLastModifiedStoredTimeStamp ()
long	getLastModifiedAlignmentTimeStampAtCreation ()
long	getLastModifiedAlignmentIdxTimeStampAtCreation ()
long	getAlignmentSizeAtCreation ()
long	getAlignmentIdxSizeAtCreation ()
boolean	isAlignmentPaired ()
double	getGlobalRPKMConstant ()
Map< String, Double >	getNumMarkers ()
Map< String, Double >	getNumberOfReads ()
Map< String, Integer >	getMaskedRegions ()
Map< String, Double >	getLambda ()
Map< String, Double >	getLocalRpkmConstant ()

Static Public Member Functions
static void	store (AlignmentDataModelStats alignmentStats) throws IOException

Static Public Attributes
static final String	SAVED_MODEL_STATS_EXT = ".srptr.aln.stats"

Protected Member Functions
boolean	isSafeToLoad ()
void	setAsUnsafeToLoad ()
void	setAsSafeToLoad ()
String	getReasonForUnsafe ()
void	setReasonForUnsafe (String reasonForUnsafe)

Detailed Description

Class that manages the storage of an AlignmentDataModelStats to permanent storage Format of the file is simple, the first line stores the timestamp of file creation the next two columns are tab separated lines containing information about the alignment and index file when the stats were stored: Size, last modified date The next line stores the global RPKM constant The next line should be a P if the alignment is paired and anything else, usually U if it is not. Then there is a line per reference sequence containing its statistics: # markers, # reads, masked regions, lambda,

Author

mgarber

Constructor & Destructor Documentation

broad.pda.seq.alignment.StoredAlignmentStats.StoredAlignmentStats

(

)

throws IOException

Member Function Documentation

long broad.pda.seq.alignment.StoredAlignmentStats.getAlignmentIdxSizeAtCreation

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long broad.pda.seq.alignment.StoredAlignmentStats.getAlignmentSizeAtCreation

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double broad.pda.seq.alignment.StoredAlignmentStats.getGlobalRPKMConstant

(

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Map<String, Double> broad.pda.seq.alignment.StoredAlignmentStats.getLambda

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long broad.pda.seq.alignment.StoredAlignmentStats.getLastModifiedAlignmentIdxTimeStampAtCreation

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long broad.pda.seq.alignment.StoredAlignmentStats.getLastModifiedAlignmentTimeStampAtCreation

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long broad.pda.seq.alignment.StoredAlignmentStats.getLastModifiedStoredTimeStamp

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Map<String, Double> broad.pda.seq.alignment.StoredAlignmentStats.getLocalRpkmConstant

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Map<String, Integer> broad.pda.seq.alignment.StoredAlignmentStats.getMaskedRegions

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Map<String, Double> broad.pda.seq.alignment.StoredAlignmentStats.getNumberOfReads

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Map<String, Double> broad.pda.seq.alignment.StoredAlignmentStats.getNumMarkers

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String broad.pda.seq.alignment.StoredAlignmentStats.getReasonForUnsafe ( )

protected

boolean broad.pda.seq.alignment.StoredAlignmentStats.isAlignmentPaired

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boolean broad.pda.seq.alignment.StoredAlignmentStats.isSafeToLoad ( )

protected

void broad.pda.seq.alignment.StoredAlignmentStats.load

(

File

alignmentStoredStatFile

)

throws NumberFormatException, IOException

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void broad.pda.seq.alignment.StoredAlignmentStats.setAsSafeToLoad ( )

protected

void broad.pda.seq.alignment.StoredAlignmentStats.setAsUnsafeToLoad ( )

protected

void broad.pda.seq.alignment.StoredAlignmentStats.setReasonForUnsafe ( String  reasonForUnsafe )

protected

static void broad.pda.seq.alignment.StoredAlignmentStats.store ( AlignmentDataModelStats  alignmentStats ) throws IOException

static

Member Data Documentation

final String broad.pda.seq.alignment.StoredAlignmentStats.SAVED_MODEL_STATS_EXT = ".srptr.aln.stats"

static

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

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