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R2012a Documentation → Bioinformatics Toolbox
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Contents

Index

• Getting Started

• User's Guide

• Functions

• Constructor

• Data Formats and Databases

• Trace Tools

• Sequence Conversion

• Sequence Utilities

• Sequence Statistics

• Sequence Visualization

• Pairwise Sequence Alignment

• Multiple Sequence Alignment

• Scoring Matrices

• Phylogenetic Tree Tools

• Phylogenetic Tree Methods

• Graph Theory

• Graph Visualization Methods

• Gene Ontology

• Gene Ontology Methods

• Protein Analysis

• Profile Hidden Markov Models

• Microarray File Formats

• Microarray Utilities

• Microarray Data Analysis and Visualization

• Microarray Normalization and Filtering

• BioIndexedFile Methods

• BioRead Methods

• BioMap Methods

• GFFAnnotation Methods

• GTFAnnotation Methods

• HeatMap Methods

• Clustergram Methods

• ExpressionSet Methods

• ExptData Methods

• DataMatrix Methods

• MetaData Methods

• MIAME Methods

• Statistical Learning

• Mass Spectrometry

• Bioanalytics

Examples

• Release Notes

saminfo - Return information about Sequence Alignment/Map (SAM) file

Syntax

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

Description

InfoStruct = saminfo(File) returns a MATLAB structure containing summary information about a SAM-formatted file.

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

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.

Input Arguments

File

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 Pair Arguments

Specify optional comma-separated pairs of Name,Value arguments, where Name is the argument name and Value is the corresponding value. Name must appear inside single quotes (' '). You can specify several name and value pair arguments in any order as Name1,Value1,...,NameN,ValueN.

'NumOfReads'

Logical that controls the inclusion of a NumReads field in InfoStruct, the output structure.

Note Setting NumOfReads to true can significantly increase the time to create the output structure.

Default: false

'ScanDictionary'

Logical that controls the scanning of the SAM-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

Output Arguments

InfoStruct

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

Field Description

Filename Name of the SAM-formatted file.

FilePath Path to the file.

FileSize Size of the file in bytes.

FileModDate Modification date of the file.

NumReads* Number of sequence reads in the file.

ScannedDictionary* Cell array of strings specifying the names of the reference sequences in the SAM-formatted file.

ScannedDictionaryCount* Cell array specifying the number of reads aligned to each reference sequence.

Header** Structure containing the file format version, sort order, and group order.

SequenceDictionary**
Structure containing the:
Sequence name
Sequence length
Genome assembly identifier
MD5 checksum of sequence
URI of sequence
Species

ReadGroup**
Structure containing the:
Read group identifier
Sample
Library
Description
Platform unit
Predicted median insert size
Sequencing center
Date
Platform

Program**
Structure containing the:
Program name
Version
Command line

* — The NumReads field is empty if you do not set the NumOfReads name-value pair argument to true. 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 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]

References

[1] Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Goncalo, A., and Durbin, R. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 16, 2078–2079.