baminfo
Return information about BAM file
Syntax
InfoStruct = baminfo(File)
InfoStruct = baminfo(File,Name,Value)
Description
returns
a MATLAB® structure containing summary information about a BAM-formatted
file.InfoStruct
= baminfo(File
)
returns
a MATLAB structure with additional options specified by one or
more InfoStruct
= baminfo(File
,Name,Value
)Name,Value
pair arguments.
Input Arguments
|
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.
|
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 Default: |
|
Logical that controls the scanning of a BAM-formatted file to
determine the number of alignment records in the file. If Default: |
Output Arguments
|
MATLAB structure containing summary information about a BAM-formatted file. The structure contains these fields.
* — The ** — 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
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. |