net.maizegenetics.dna.tag

Interface Reads

All Known Implementing Classes:

ReadsByTaxa

public interface Reads

Basic methods for working with nextgen reads

Author:

edbuckler

Method Summary

Modifier and Type	Method and Description
boolean	areReadsUnique() Reports whether this list of reads includes duplicates True is there are no read duplicates, false otherwise.
long[]	getRead(int index) Get the compressed read sequence in a long array for a given index
int	getReadCount(int index) Gets the count of a particular read.
int	getReadIndex(long[] read) Gets the first index of a read (the only one if a unique list).
int[]	getReadIndexSet(long[] read) Gets the set indices of matching reads (the only one if a unique list).
int	getReadTotal() This is the number of different reads in the list (NOT THE SUM OF THE COUNTS) The index will vary from 0 to (ReadTotal-1) This is the number of distinct reads if readUnique is true

Method Detail

getRead

long[] getRead(int index)

Get the compressed read sequence in a long array for a given index

Parameters:

index -

Returns:

compressed read sequence in long array

getReadCount

int getReadCount(int index)

Gets the count of a particular read. If index does not exist it return -1

Parameters:

index -

Returns:

read count

getReadIndex

int getReadIndex(long[] read)

Gets the first index of a read (the only one if a unique list). If the read is not found then it return a negative value indicating its insertion point.

Parameters:

read - as a compressed long array

Returns:

the index of the read in the array

getReadIndexSet

int[] getReadIndexSet(long[] read)

Gets the set indices of matching reads (the only one if a unique list). If the read is not found then it returns a null array indicating its insertion point.

Parameters:

read - as a compressed long array

Returns:

set of indices of the read in the array (or null)

areReadsUnique

boolean areReadsUnique()

Reports whether this list of reads includes duplicates True is there are no read duplicates, false otherwise. Collapses read files are likely to be unique While a virtual digest of a genome with contain some duplicates

Returns:

getReadTotal

int getReadTotal()

This is the number of different reads in the list (NOT THE SUM OF THE COUNTS) The index will vary from 0 to (ReadTotal-1) This is the number of distinct reads if readUnique is true

Returns:

total number of reads