[nilshomer]

. I know it is trivial to convert SAM/BAM to MVF, but given the large amount of data (maybe >1TB data), most users would prefer viewing the alignment directly rather than duplicate them again.

I have to reiterate the point lh3 is making. SAM/BAM format would be great if you could support it, since even people outside of 1000 genomes have generated 100's of GBs of data in SAM/BAM. Also, paired end info, indels, quality scores, complex references, and the ability to add arbitrary annotation and post-alignment "tracks" (maybe interact with a backend database?) would be the killer application.

[bioinfosm]

congrats baohua!
It would be great if you could keep a running log of changes for newer versions

[baohua100]

The paper is published on Bioinformaitcs.

MapView: visualization of short reads alignment on a desktop computer

http://bioinformatics.oxfordjournals...bstract/btp255

[lparsons]

I ran the software on Windows, and was able to get it running. However, after converting a MAQ alignment to MVF, when I load the MVF file, I get an error:

Arithmetic operation resulted in an overflow.

[lparsons]

I tried to run MapView using Mono on a Mac OS X 10.5. It started, displayed the window briefly, the crashed with this error:

System.NotImplementedException: The requested feature is not implemented.
at System.Windows.Forms.XplatUICarbon.get_CursorSize () [0x00000]
at System.Windows.Forms.XplatUI.get_CursorSize () [0x00000]
at System.Windows.Forms.SystemInformation.get_CursorSize () [0x00000]
at MapView.Form1.abmmeKAlo (System.Object , System.EventArgs ) [0x00000]
at System.Windows.Forms.Form.OnLoad (System.EventArgs e) [0x00000]
at System.Windows.Forms.Form.OnLoadInternal (System.EventArgs e) [0x00000]
Segmentation fault

Any suggestions? Thanks.

[baohua100]

Thanks for your reply! MapView 3.1.2 only support for visualization of ungapped alignment. We will add the function of gapped and spliced alignment later.

First, I would like to thank you guys for this useful tool. I have tried it on several datasets and found its performance to be more than adequate. I have one question: I have noticed that the viewer handles the alignments as ungapped even if I feed it with gapped ones (like soap1 or seqmap outputs). Actually, the very nature of input information for the viewer suggests that it positions only the first base of a read against reference sequence, but not every base. So, I wonder if you have any plans to make Mapview to visualize indels?

[baohua100]

Thanks! bioinform! Sorry, there is not a command-line version using x-windows now.

Thanks baohua.
Whats the changelog? Is there a command-line version using x-windows maybe?

[garwuf]

indels

First, I would like to thank you guys for this useful tool. I have tried it on several datasets and found its performance to be more than adequate. I have one question: I have noticed that the viewer handles the alignments as ungapped even if I feed it with gapped ones (like soap1 or seqmap outputs). Actually, the very nature of input information for the viewer suggests that it positions only the first base of a read against reference sequence, but not every base. So, I wonder if you have any plans to make Mapview to visualize indels?

[bioinfosm]

Thanks baohua.
Whats the changelog? Is there a command-line version using x-windows maybe?

[baohua100]

MapView 3.1.2 is released!

If you have some suggestions or bugs, please post here! Thanks!

[WJW-Davy]

Welcome to test MapView 3.1.0.0

MapView is quick and using small memory. Good performance.

MapView is based on .NET Framework. You can try it on Windows (with .NET 2.0 or higher) and Linux (with Mono 2.0 or higher).

Welcome to test MapView 3.1.0.0

Download: http://evolution.sysu.edu.cn/mapview/

[WJW-Davy]

MapView 3.0 beta1 is being tested...

MapView 3.0 beta2 is being tested.
MapView 3.0 has improved much. Quality Score, Paired-end data, structure variation, coverage distribution, quality distribution, text quick view, zoom in/out, and other features are supported.

[lh3]

This sounds very promising! I just wonder if you are interested in natively supporting the SAM/BAM format. I think the 1000genomes project has already released some alignments in the BAM format and yet more to come in the next few months. I know it is trivial to convert SAM/BAM to MVF, but given the large amount of data (maybe >1TB data), most users would prefer viewing the alignment directly rather than duplicate them again. BAM is also compressed and indexable, and supports indels and long alignments. Sorry if this sounds like promoting projects related to myself.

[guohui]

To Aengus,

Next version of MapView is in debugging period and will be available soon. The new version will support the display of quality score and pair-end data.

[Aengus]

Hi guys,

Just after a quick update.

Is the display of quality scores now in the download? The main page still says that the version is 1.0


Regards
Aengus