baminfo

Return information about BAM file

Syntax

InfoStruct = baminfo(File) InfoStruct = baminfo(File,Name,Value)

Description

InfoStruct = baminfo(File) returns a MATLAB^® structure containing summary information about a BAM-formatted file.

InfoStruct = baminfo(File,Name,Value) returns a MATLAB structure with additional options specified by one or more Name,Value pair arguments.

Input Arguments

File

Character vector or string specifying a file name or path and file name of a BAM-formatted file. If you specify only a file name, that file must be on the MATLAB search path or in the Current Folder.

Name-Value Arguments

Specify optional pairs of arguments as Name1=Value1,...,NameN=ValueN, where Name is the argument name and Value is the corresponding value. Name-value arguments must appear after other arguments, but the order of the pairs does not matter.

Before R2021a, use commas to separate each name and value, and enclose Name in quotes.

ScanDictionary

Logical that controls the scanning of the BAM-formatted file to determine the reference names and the number of reads aligned to each reference. If true, the ScannedDictionary and ScannedDictionaryCount fields contain this information.

Default: false

NumOfReads

Logical that controls the scanning of a BAM-formatted file to determine the number of alignment records in the file. If true, the NumReads field contains this information.

Default: false

Output Arguments

InfoStruct

MATLAB structure containing summary information about a BAM-formatted file. The structure contains these fields.

Field	Description
`Filename`	Name of the BAM-formatted file.
`FilePath`	Path to the file.
`FileSize`	Size of the file in bytes.
`FileModDate`	Modification date of the file.
`Header`**	Structure containing the file format version, sort order, and group order.
`ReadGroup`**	Structure containing the: Read group identifier Sample Library Description Platform unit Predicted median insert size Sequencing center Date Platform
`SequenceDictionary`**	Structure containing the: Sequence name Sequence length Genome assembly identifier MD5 checksum of sequence URI of sequence Species
`Program`**	Structure containing the: Program name Version Command line
`NumReads`	Number of reference sequences in the BAM-formatted file.
`ScannedDictionary`*	Cell array of character vectors specifying the names of the reference sequences in the BAM-formatted file.
`ScannedDictionaryCount`*	Cell array specifying the number of reads aligned to each reference sequence.

* — The ScannedDictionary and ScannedDictionaryCount fields are empty if you do not set the ScanDictionary name-value pair argument to true.

** — These structures and their fields appear in the output structure only if they are in the BAM file. The information in these structures depends on the information in the BAM file.

Examples

collapse all

Retrieve information about a BAM file

Open Live Script

This example shows how to retrieve information about the ex1.bam file included with the Bioinformatics Toolbox™.

info = baminfo('ex1.bam','ScanDictionary',true,'numofreads',true)

info = struct with fields:
                  Filename: 'ex1.bam'
                  FilePath: '/mathworks/devel/bat/Bdoc22a/build/matlab/toolbox/bioinfo/bioinfodata'
                  FileSize: 126692
               FileModDate: '07-May-2010 16:12:05'
                    Header: [1x1 struct]
                 ReadGroup: [1x2 struct]
        SequenceDictionary: [1x2 struct]
                  NumReads: 3307
         ScannedDictionary: {2x1 cell}
    ScannedDictionaryCount: [2x1 uint64]

List the number of references found in the BAM file.

numel(info.ScannedDictionary)

ans = 2

Alternatively, you can use the available header information from a BAM file to find out the number of references, thus avoiding the whole traversal of the source file.

info = baminfo('ex1.bam'); 
NRefs = numel(info.SequenceDictionary)

NRefs = 2

Tips

Use baminfo to investigate the size and content of a BAM-formatted file, including reference sequence names, before using the bamread function to read the file contents into a MATLAB structure.

Version History

Introduced in R2010b