broad.pda.countreads.FastqLibraryStats Class Reference

Public Member Functions
	FastqLibraryStats (String singleReadFastq) throws IOException
	FastqLibraryStats (String read1fastq, String read2fastq) throws IOException
int	getNumUniqueReads ()
double	getPercentDuplicated ()
int	getTotalReads ()
long	getEstimatedLibrarySize ()
void	writeSeparateFiles (String outUniquePrefix, String outDupPrefix, boolean pairedReads) throws IOException

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

Detailed Description

Author

prussell

Constructor & Destructor Documentation

broad.pda.countreads.FastqLibraryStats.FastqLibraryStats

(

String

singleReadFastq

)

throws IOException

Constructor for single end reads

Parameters

singleReadFastq

Exceptions

IOException

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broad.pda.countreads.FastqLibraryStats.FastqLibraryStats	(	String	read1fastq,
		String	read2fastq
	)		throws IOException

Constructor for paired end reads

Parameters

read1fastq
read2fastq

Exceptions

IOException

Member Function Documentation

long broad.pda.countreads.FastqLibraryStats.getEstimatedLibrarySize

(

)

Get the estimated library size based on number of reads and percent duplicates

Returns

The estimated library size

int broad.pda.countreads.FastqLibraryStats.getNumUniqueReads

(

)

Get the number of unique reads

Returns

The number of unique reads

double broad.pda.countreads.FastqLibraryStats.getPercentDuplicated

(

)

Get the proportion of reads that are duplicates

Returns

The proportion of reads that are duplicated

int broad.pda.countreads.FastqLibraryStats.getTotalReads

(

)

Get the total number of reads

Returns

The total number of reads

static void broad.pda.countreads.FastqLibraryStats.main ( String[]  args ) throws IOException

static

Parameters

args

Exceptions

IOException

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void broad.pda.countreads.FastqLibraryStats.writeSeparateFiles	(	String	outUniquePrefix,
		String	outDupPrefix,
		boolean	pairedReads
	)		throws IOException

Write fastq files of unique reads and duplicated reads

Parameters

outUniquePrefix	Output fastq file of unique reads
outDupPrefix	Output fastq file of duplicated reads
pairedReads	Whether the reads are paired

Exceptions

IOException

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

• java/broad/pda/countreads/FastqLibraryStats.java