.NET Bio 1.01

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Downloads: 2628
Change Set: 73946
Released: Apr 16, 2012
Updated: May 17, 2012 by sjmercer
Dev status: Stable Help Icon

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Application .NET Bio 1.01
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Application .NET Bio Sequence Assembler 1.01
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Application .NET Bio Biology Extension for Excel 1.01
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Documentation .NET Bio V1 Training Materials
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Release Notes

Version 1.01, April 2012

Application-specific release notes are installed with each application - the notes below refer to the .NET Bio 1.01 libraries themselves.

.NET Bio is an open source, reusable .NET library and application programming interface (API) for bioinformatics.

.NET Bio is available at http://bio.codeplex.com. It is licensed under the OSI approved Apache 2.0 License, a copy of which may be found here: http://bio.codeplex.com/license.

KNOWN ISSUES
============
- Current issues are listed here: http://bio.codeplex.com/workitem/list/advanced

- Any single RNA, DNA, or protein sequence in .NET Bio is limited to a length of 2 billion characters. The largest human chromosome is 250Mbp so the single sequence limit should NOT be a limiting factor in your development. If you experience issues related with this limit please post on the issue tracker tab on the Codeplex site. This is not a data size limit for the assembly process.

CHANGES FROM VERSION 1.0 TO VERSION 1.01
===============================

Breaking Changes

- .NET Bio no longer autodetects the subtype of a FASTQ file. This is due to a change in quality scoring between versions 1.5 and 1.8 of the Illumina FASTQ file format, preventing .NET Bio from automatically distinguishing between these formats.

- The ISequenceRangeParser has renamed the FileTypes property to SupportedFileTypes for the interface and single implementation (BedParser).

- ISequenceRangeParser now derives from IParser for conformity.

- The RegisteredAddIn.GetAlphabets() method has been removed. The functionality was moved to a private method on the Alphabets class. You should just use Alphabets.All to retrieve the list of custom alphabets

- The BioExcel add-in imports data to worksheets differently. If you depend on the order of rows + cells, you will need to adjust your scripts.

Non-breaking changes

- .NET Bio now supports the SFF (Standard Flowgram Format) in support of sequences generated by the Roche 454 sequencer.

- The Bio.Hpc.Distributeapp.exe has been renamed to be DistributeApp.exe

- The FileFormatConverter.exe is now installed into the Tools directory

- Several new extension methods have been added to Bio.dll
ISequence.ConvertToString
IAlphabet.CheckIsTermination(byte/char)
IAlphabet.CheckIsGap(char)
IAlphabet.CheckIsAmbiguous(char)
IAlphabet.GetFriendlyName(char)

- SAMBAM parser and formatter have been updated to support new CIGAR and additional optional fields according to specification 1.4.

- Several bugs from 1.0 were resolved in this release; please refer to http://bio.codeplex.com/workitem/list/advanced for details

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