saminfo
Return information about SAM file
Syntax
InfoStruct
= saminfo(File
)
InfoStruct = saminfo(File,Name,Value)
Description
returns
a MATLAB® structure containing summary information about a SAM-formatted
file.InfoStruct
= saminfo(File
)
returns
a MATLAB structure with additional options specified by one or
more InfoStruct
= saminfo(File
,Name,Value
)Name,Value
pair arguments.
Input Arguments
| Character vector or string specifying a file name or path and file name of a SAM-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
Output Arguments
| MATLAB structure containing summary information about a SAM-formatted file. The structure contains these fields.
* — The ** — These structures and their fields appear in the output structure only if they are in the SAM file. The information in these structures depends on the information in the SAM file. |
Examples
Return information about the ex1.sam
file
included with Bioinformatics Toolbox™:
info = saminfo('ex1.sam')
info = Filename: 'ex1.sam' FilePath: [1x89 char] FileSize: 254270 FileModDate: '12-May-2011 14:23:25' Header: [1x1 struct] SequenceDictionary: [1x1 struct] ReadGroup: [1x2 struct] NumReads: [] ScannedDictionary: {0x1 cell} ScannedDictionaryCount: [0x1 uint64]
Return information about the ex1.sam
file
including the number of sequence reads:
info = saminfo('ex1.sam','numofreads', true)
info = Filename: 'ex1.sam' FilePath: [1x89 char] FileSize: 254270 FileModDate: '12-May-2011 14:23:25' Header: [1x1 struct] SequenceDictionary: [1x1 struct] ReadGroup: [1x2 struct] NumReads: 1501 ScannedDictionary: {0x1 cell} ScannedDictionaryCount: [0x1 uint64]
Tips
Use saminfo to investigate the size and
content of a SAM file before using the samread function
to read the file contents into a MATLAB structure. |
Version History
Introduced in R2010a
See Also
samread
| fastqread
| fastqwrite
| fastqinfo
| fastainfo
| fastaread
| fastawrite
| sffinfo
| sffread
| BioIndexedFile
| BioMap