baminfo
Return information about BAM file
Description
returns a MATLAB® structure containing summary information about a BAM-formatted
file.InfoStruct
= baminfo(File
)
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.
specifies additional options using one or more name-value arguments. For example, to
return the number of alignment records, InfoStruct
= baminfo(File
,Name,Value
)InfoStruct =
baminfo(File,NumOfReads=true)
.
Examples
Retrieve information about a BAM file
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/filer/batfs2561-0/Bdoc24b.2679053/build/runnable/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
Input Arguments
File
— Path to BAM-formatted file
string | character vector
Path to BAM-formatted file, specified as a character vector or string specifying a file name or path and file name of a file. If you specify only a file name, that file must be on the MATLAB search path or in the current folder.
Example: "C:\Documents\bamfile.bam"
Data Types: char
| string
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.
Example: InfoStruct =
baminfo("ex1.bam",ScanDictionary=true,NumOfReads=true)
Names are case-insensitive. For example, you can use
"numofreads"
instead of
"NumOfReads"
.
NumOfReads
— Indication to determine the number of alignment records in the file
false
(default) | true
Indication to determine the number of alignment records in the file,
specified as false
or true
. If
true
, the NumReads
field of
InfoStruct
in contains this
information.
Example: true
Data Types: logical
ScanDictionary
— Indication to determine the number of alignment records in the file
false
(default) | true
Indication to determine the reference names and the number of reads
aligned to each reference.File
, specified as
false
(do not determine) or
true
. If true
, the
ScannedDictionary
and
ScannedDictionaryCount
fields of
InfoStruct
contain this information.
Example: true
Data Types: logical
Output Arguments
InfoStruct
— Summary information about a BAM-formatted file
structure
Summary information about a BAM-formatted file, returned as a MATLAB structure. 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:
|
SequenceDictionary ** | Structure containing the:
|
Program ** | Structure containing the:
|
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.
Version History
Introduced in R2010b
See Also
External Websites
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