Documentation

This is machine translation

Translated by Microsoft
Mouseover text to see original. Click the button below to return to the English verison of the page.

Note: This page has been translated by MathWorks. Please click here
To view all translated materals including this page, select Japan from the country navigator on the bottom of this page.

filterByFlag

Class: BioMap

Filter sequence reads by SAM flag

Syntax

Indices = filterByFlag(BioObj, FlagName, FlagValue)
Indices = filterByFlag(BioObj, Subset, FlagName, FlagValue)
Indices = filterByFlag(..., FlagName1, FlagValue1, FlagName2, FlagValue2, ...)

Description

Indices = filterByFlag(BioObj, FlagName, FlagValue) returns Indices, a vector of logical indices, indicating the read sequences in BioObj, a BioMap object, with FlagName set to FlagValue.

Indices = filterByFlag(BioObj, Subset, FlagName, FlagValue) returns Indices, a vector of logical indices, indicating the read sequences that meet the specified criteria from a subset of entries in a BioMap object.

Indices = filterByFlag(..., FlagName1, FlagValue1, FlagName2, FlagValue2, ...) applies multiple flag filters in a single statement.

Input Arguments

BioObj

Object of the BioMap class.

Subset

Either of the following to specify a subset of the elements in BioObj:

  • Vector of positive integers

  • Logical vector

FlagName

Character vector specifying one of the following flags to filter by:

  • 'pairedInSeq' — The read is paired in sequencing, regardless if it is mapped as a pair.

  • 'pairedInMap' — The read is mapped in a proper pair.

  • 'unmappedQuery' — The read is unmapped.

  • 'unmappedMate' — The mate is unmapped.

  • 'strandQuery' — Strand direction of the read (0 = forward, 1 = reverse).

  • 'strandMate' — Strand direction of the mate (0 = forward, 1 = reverse).

  • 'readIsFirst' — The read is first in a pair.

  • 'readIsSecond' — The read is second in a pair.

  • 'alnNotPrimary' — The read's alignment is not primary.

  • 'failedQualCheck' — The read fails platform or vendor quality checks.

  • 'duplicate' — The read is a PCR or optical duplicate.

FlagValue

Logical value indicating the status of a flag. A 0 indicates false or forward, and a 1 indicates true or reverse.

Output Arguments

Indices

Vector of logical indices, indicating the read sequences in BioObj with FlagName set to FlagValue.

Examples

Construct a BioMap object, and then determine the read sequences that are both mapped in a proper pair and first in a pair:

% Construct a BioMap object from a SAM file 
BMObj1 = BioMap('ex1.sam');
% Filter the elements using 'pairedInMap' and 'readIsFirst' flags 
Indices = filterByFlag(BMObj1, 'pairedInMap', true,...
                       'readIsFirst', true);
% Return the headers of the filtered elements
filtered_Headers = BMObj1.Header(Indices);
Was this topic helpful?