setHeader

Update header information of reads

collapse all in page

Syntax

newObject = setHeader(object,headerInfo)
newObject = setHeader(object,headerInfo,subset)

Description

newObject = setHeader(object,headerInfo) returns a new object that is a copy of object with the Header property set to headerInfo.

example

newObject = setHeader(object,headerInfo,subset) returns a new object that is a copy of object with the Header property of a subset of elements set to headerInfo. A one-to-one relationship must exist between the number and order of elements in headerInfo and subset.

example

Examples

collapse all

Open Live Script

Store read data from a SAM-formatted file in a BioRead object. Set 'InMemory' to true to load the object into memory so that you can modify its properties.

br = BioRead('SRR005164_1_50.fastq','InMemory',true)
br = 
  BioRead with properties:

     Quality: {50×1 cell}
    Sequence: {50×1 cell}
      Header: {50×1 cell}
       NSeqs: 50
        Name: ''

Check the header information for the first three elements of the object.

br.Header(1:3)
ans = 3×1 cell
    {'SRR005164.1'}
    {'SRR005164.2'}
    {'SRR005164.3'}

Define custom headers for the first three elements.

headers = {'Header1','Header2','Header3'};

Set the header information of the first three elements. br2 is a copy of br with the headers updated. If you need to update the br object itself, set it as the output of the function.

br2 = setHeader(br,headers,[1:3]);
br2.Header(1:3)
ans = 3×1 cell
    {'Header1'}
    {'Header2'}
    {'Header3'}

You can also update the headers of the br object directly using dot notation.

br.Header(1:3) = headers;
br.Header(1:3)
ans = 3×1 cell
    {'Header1'}
    {'Header2'}
    {'Header3'}

Input Arguments

collapse all

Object containing the read data, specified as a BioRead or BioMap object. If the object is not stored in memory, you cannot modify its properties, except the Name property.

Example: readData

Header information of the reads, specified as a cell array of character vectors or string vector.

Example: {'H1','H2','H3'}

Subset of elements in the object, specified as a vector of positive integers, logical vector, string vector, or cell array of character vectors containing valid sequence headers.

Example: [1 3]

Tip

When you use a sequence header (or a cell array of headers) for subset, a repeated header specifies all elements with that header.

Output Arguments

collapse all

New object with updated properties, returned as a BioRead or BioMap object.

Version History

Introduced in R2010a

See Also

|

Topics