Version 4.0 (R2011b) Bioinformatics Toolbox Software

This table summarizes what's new in Version 4.0 (R2011b):

New Features and Changes	Version Compatibility Considerations	Fixed Bugs and Known Problems
Yes Details below	Yes—Details labeled as Compatibility Considerations, below. See also Summary.	Bug Reports Includes fixes

New and updated features in this version include:

• Visualizing and Investigating Short-Read Alignments and Feature Annotations in the NGS Browser

• Objects for Genomic Feature Annotations

• Enhancements to BioRead and BioMap Objects

• Enhancements to the saminfo and baminfo Functions

• Conversion of Error and Warning Message Identifiers

• Function Elements Being Removed

Visualizing and Investigating Short-Read Alignments and Feature Annotations in the NGS Browser

The NGS Browser lets you visually verify and investigate the alignment of short-read sequences to a reference sequence. For more information, see Visualizing and Investigating Short-Read Alignments and ngsbrowser.

Objects for Genomic Feature Annotations

Following are new classes for objects that contain genomic feature annotations for nucleotide sequences:

• GFFAnnotation — Contain data from GFF file.

• GTFAnnotation — Contain data from GTF file.

These classes have properties and methods that you can use to explore, access, filter, and manipulate all or a subset of the feature annotation data. For more information, see Storing and Managing Feature Annotations in Objects.

Enhancements to BioRead and BioMap Objects

You can now construct a BioMap object from a BAM-formatted file.

When constructing these objects from source files, by default the data is indexed, which is more efficient for construction and data access. The BioRead and BioMap constructors now include an IndexDir name-value pair argument, which lets you specify the location of the index file.

You can still construct these objects with the data in memory, which lets you modify all the properties of the objects. The BioRead and BioMap constructors now include an InMemory name-value pair argument, which lets you construct the objects with the data in memory.

For details on the previous enhancements, see Storing and Managing Short-Read Sequence Data in Objects.

Compatibility Considerations

The BioRead and BioMap constructors are changed as follows:

• The following syntaxes that take a BioIndexedFile object as an input will be removed in a future release:

  BioReadobj = BioRead(BioIFobj)

  BioMapobj = BioMap(BioIFobj)

  There is no longer a need to use this syntax, as you can create an indexed object directly from the SAM- or BAM-formatted source file. See Representing Sequence and Quality Data in a BioRead Object or Representing Sequence, Quality, and Alignment/Mapping Data in a BioMap Object.

• The following syntaxes will be removed in a future release:

  BioReadobj = BioRead('SAMFile', File)

  BioReadobj = BioRead('FASTQFile', File)

  Use this syntax instead:

  BioReadobj = BioRead(File)

• The following syntax will be removed in a future release:

  BioMapobj = BioMap('SAMFile', File)

  Use this syntax instead:

  BioMapobj = BioMap(File)

• The Indexed name-value pair argument as input to the getSubset method of the BioRead or BioMap class will be removed in a future release. Use the InMemory name-value pair argument instead.

• The 'SubsetRef' name-value pair argument of the BioMap constructor will be removed in a future release. Use the 'SelectRef' name-value pair argument instead.

• If you use the getSubset method of a BioRead or BioMap object, and specify the same element more than once, the method errors, even if the object is in memory.

Enhancements to the saminfo and baminfo Functions

The saminfo and baminfo functions now include a ScanDictionary name-value pair argument, which controls the return of the reference names and the number of reads aligned to each reference from a SAM- or BAM-formatted file in new fields, ScannedDictionary and ScannedDictionaryCount. This information is needed when constructing a BioMap object from a file with multiple reference sequences. For more information, see Constructing a BioMap Object from a SAM- or BAM-Formatted File.

Compatibility Considerations

The Reference field is no longer returned in the output structure for baminfo. The ScannedDictionary field now includes names of the reference sequences.

Conversion of Error and Warning Message Identifiers

For R2011b, some error and warning message identifiers have changed in Bioinformatics Toolbox™.

Compatibility Considerations

If you have scripts or functions that use message identifiers that changed, you must update the code to use the new identifiers. Typically, message identifiers are used to turn off specific warning messages, or in code that uses a try/catch statement and performs an action based on a specific error identifier.

For example, the Bioinfo:nwalign:InvalidScoringMatrix identifier has changed to bioinfo:nwalign:InvalidScoringMatrix. If your code checks for Bioinfo:nwalign:InvalidScoringMatrix, you must update it to check for bioinfo:nwalign:InvalidScoringMatrix instead.

To determine the identifier for a warning, run the following command just after you see the warning:

[MSG,MSGID] = lastwarn;

The preceding command saves the message identifier to the variable MSGID.

To determine the identifier for an error, run the following command just after you see the error:

exception = MException.last;

MSGID = exception.identifier;

Note   Warning messages indicate a potential issue with your code. While you can turn off a warning, a suggested alternative is to change your code so it runs warning-free.

Function Elements Being Removed

Function Element Name	What Happens When You Use This Function Element	Use This Instead	Compatibility Considerations
'SubsetRef' name-value pair argument as input to BioMap constructor function	Warns	'SelectRef' name-value pair argument	See the Compatibility Considerations subheading in Enhancements to BioRead and BioMap Objects.
BioIndexedFile object as input to the BioRead or BioMap constructor function	Warns	A FASTQ-, SAM-, or BAM-formatted file	See the Compatibility Considerations subheading in Enhancements to BioRead and BioMap Objects.
'FASTQFile', File pair as input to the BioRead constructor	Warns	File	See the Compatibility Considerations subheading in Enhancements to BioRead and BioMap Objects
'SAMFile', File pair as input to the BioRead or BioMap constructor	Warns	File	See the Compatibility Considerations subheading in Enhancements to BioRead and BioMap Objects.
Indexed name-value pair argument as input to getSubset method of the BioRead or BioMap class	Warns	InMemory name-value pair argument	See the Compatibility Considerations subheading in Enhancements to BioRead and BioMap Objects.
Reference field of structure returned by baminfo	Errors	ScannedDictionary field	See the Compatibility Considerations subheading in Enhancements to the saminfo and baminfo Functions.

Version 4.1 (R2012a) Bioinformatics Toolbox Software

Version 3.7 (R2011a) Bioinformatics Toolbox Software

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