broad.pda.seq.rap.rna.CollectRnaSeqMetrics Class Reference

Inheritance diagram for broad.pda.seq.rap.rna.CollectRnaSeqMetrics:

Collaboration diagram for broad.pda.seq.rap.rna.CollectRnaSeqMetrics:

Static Public Member Functions
static void	main (final String[] argv)

Public Attributes
final String	USAGE
File	EXCLUDE_BED =null
File	EXCLUDE_REGION_FILE =null
Integer	BUFFER = 1000

Protected Member Functions
void	setup (final SAMFileHeader header, final File samFile)
void	acceptRead (final SAMRecord rec, final ReferenceSequence refSeq)
void	finish ()

Member Function Documentation

void broad.pda.seq.rap.rna.CollectRnaSeqMetrics.acceptRead ( final SAMRecord  rec, final ReferenceSequence  refSeq  )

protected

void broad.pda.seq.rap.rna.CollectRnaSeqMetrics.finish ( )

protected

static void broad.pda.seq.rap.rna.CollectRnaSeqMetrics.main ( final String[]  argv )

static

Required main method implementation.

void broad.pda.seq.rap.rna.CollectRnaSeqMetrics.setup ( final SAMFileHeader  header, final File  samFile  )

protected

Member Data Documentation

Integer broad.pda.seq.rap.rna.CollectRnaSeqMetrics.BUFFER = 1000

File broad.pda.seq.rap.rna.CollectRnaSeqMetrics.EXCLUDE_BED =null

File broad.pda.seq.rap.rna.CollectRnaSeqMetrics.EXCLUDE_REGION_FILE =null

final String broad.pda.seq.rap.rna.CollectRnaSeqMetrics.USAGE

Initial value:

= getStandardUsagePreamble() +
            "Program to collect metrics about the alignment of RNA to various functional classes of loci in the genome:" +
            " coding, intronic, UTR, intergenic, ribosomal.\n" +
            "Also determines strand-specificity for strand-specific libraries.\n" +
            "For RAP, provide a EXCLUDE_REGION specifying the bounds of the target RNA.  Metrics will be calculated excluding this region."

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

• java/broad/pda/seq/rap/rna/CollectRnaSeqMetrics.java