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Old 06-04-2009, 01:46 AM   #81
mikyatope
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^ Indeed, it was GDIplus , thanks !
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Old 06-04-2009, 08:02 AM   #82
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Hi, Fabio
Thank you for your message.
I have tested three files on Windows about "Coverage Distribution". All of them were OK.
But on linux, two of them were OK and another one got "Unhandled Exception" after the list had shown.

The "Unhandled Exception" on Linux about "Coverage Distribution" confused me. I will try to do coverage analysis on linux in another way.
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Old 06-05-2009, 07:37 AM   #83
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Default MapView 3.4.1 for Windows and Linux

Download link1: https://sites.google.com/site/wjwdav...attredirects=0

3.4.1 [2009.6.5]
Coverage analysis (Statistics->Coverage Distribution) changed in order to avoid "Unhandled Exception" on Linux.
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Old 06-08-2009, 08:25 PM   #84
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Two questions about this program -
1) will it handle 454 reads and contigs, please?
2) running it on Ubuntu 8.04 gave the following error messages:

** (MapView.exe:19020): WARNING **: The following assembly referenced from ~/backup/MapView.exe could not be loaded:
Assembly: System.Windows.Forms (assemblyref_index=0)
Version: 2.0.0.0
Public Key: b77a5c561934e089
The assembly was not found in the Global Assembly Cache, a path listed in the MONO_PATH environment variable, or in the location of the executing assembly (~/backup/).

** (MapView.exe:19020): WARNING **: Could not load file or assembly 'System.Windows.Forms, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089' or one of its dependencies.

** (MapView.exe:19020): WARNING **: Missing method EnableVisualStyles in assembly ~/backup/MapView.exe, type System.Windows.Forms.Application

Unhandled Exception: System.IO.FileNotFoundException: Could not load file or assembly 'System.Windows.Forms, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089' or one of its dependencies.
File name: 'System.Windows.Forms, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089'

I presume this is a Mono issue? I have not used Mono or .NET before. Thank you!
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Old 06-08-2009, 09:11 PM   #85
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Quote:
Originally Posted by habm View Post
Two questions about this program -
1) will it handle 454 reads and contigs, please?
2) running it on Ubuntu 8.04 gave the following error messages:

** (MapView.exe:19020): WARNING **: The following assembly referenced from ~/backup/MapView.exe could not be loaded:
Assembly: System.Windows.Forms (assemblyref_index=0)
Version: 2.0.0.0
Public Key: b77a5c561934e089
The assembly was not found in the Global Assembly Cache, a path listed in the MONO_PATH environment variable, or in the location of the executing assembly (~/backup/).

** (MapView.exe:19020): WARNING **: Could not load file or assembly 'System.Windows.Forms, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089' or one of its dependencies.

** (MapView.exe:19020): WARNING **: Missing method EnableVisualStyles in assembly ~/backup/MapView.exe, type System.Windows.Forms.Application

Unhandled Exception: System.IO.FileNotFoundException: Could not load file or assembly 'System.Windows.Forms, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089' or one of its dependencies.
File name: 'System.Windows.Forms, Version=2.0.0.0, Culture=neutral, PublicKeyToken=b77a5c561934e089'

I presume this is a Mono issue? I have not used Mono or .NET before. Thank you!

For solexa reads only.
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Old 06-08-2009, 11:13 PM   #86
WJW-Davy
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Default Mono on Ubuntu

Mono on Ubuntu:

First of all you must to install some packages. Choose "Applications->Accessories->Terminal". In the console write:

Code:
sudo apt-get install libmono-winforms2.0-cil
Write your password and software will download & install some files. Don't close the console.

Now you are able to use MapView. Just write

Code:
mono MapView.exe
The above command works only if you have saved MapView.exe file into your home directory. If you have saved the file into the desktop you must write:

Code:
mono Desktop/MapView.exe
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Last edited by WJW-Davy; 06-09-2009 at 12:49 AM.
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Old 06-09-2009, 01:41 AM   #87
fabio.marroni
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Default Coverage Issues

I tried the new 3.4.1 version in Ubuntu; it analyzes coverage distribution without crashing, even on very large files!

However, in both old and new version, I noticed some problems when counting very high sequence coverage. If coverage is higher than 65536 (2^16), then the software restarts counting from one.
I attach a small table with an example. In the first column you will find the experiment number, one for each illumina tag, and in the second column you will find the coverage. I had 12 pools (one for tag), each one with a certain coverage (lower than 65536), and they summed up to a coverage of 66541. When visualizing the total sample I have for the same position a coverage of 1005, which is exactly 66541-65536.

Can you help us with this issue?
Thank you very much
Attached Files
File Type: txt example.txt (140 Bytes, 7 views)
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Old 06-09-2009, 01:54 AM   #88
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Quote:
Originally Posted by fabio.marroni View Post
I tried the new 3.4.1 version in Ubuntu; it analyzes coverage distribution without crashing, even on very large files!

However, in both old and new version, I noticed some problems when counting very high sequence coverage. If coverage is higher than 65536 (2^16), then the software restarts counting from one.
I attach a small table with an example. In the first column you will find the experiment number, one for each illumina tag, and in the second column you will find the coverage. I had 12 pools (one for tag), each one with a certain coverage (lower than 65536), and they summed up to a coverage of 66541. When visualizing the total sample I have for the same position a coverage of 1005, which is exactly 66541-65536.

Can you help us with this issue?
Thank you very much
MapView used only 2 bytes (16bits) to represent the number of coverage. So the max coverage was 65535. I will expand it later.
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Old 06-30-2009, 12:44 AM   #89
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Default How to convert to MVR files?

Dear baohua & Davy:

I have MAQ files converted to MVF format for visualizing, but how do I get MVR files? I used Statistics->SNP result list, but get a error message:

Code:
  <1>  2009-6-30 16:01:13 
No MVR file!

  <2>  2009-6-30 16:02:46 
No SNP results!
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Old 06-30-2009, 03:37 AM   #90
baohua100
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Quote:
Originally Posted by hard998 View Post
Dear baohua & Davy:

I have MAQ files converted to MVF format for visualizing, but how do I get MVR files? I used Statistics->SNP result list, but get a error message:

Code:
  <1>  2009-6-30 16:01:13 
No MVR file!

  <2>  2009-6-30 16:02:46 
No SNP results!
You should run SNP detection (on the right panel) first!
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Old 08-13-2009, 08:15 AM   #91
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Default MapView not working for paired reads

Hello,

I would like to visualise some paired reads data using MapView. I have tried to use MVFmaker and choose the checkbox of Paired-end data. However, this checkbox is greyed out and I cannot select it.

I am using MapView version 3.4.1 under ubuntu, using mono, and it seems to work fine otherwise. Can anyone tell me how to create the MVF file for my paired reads? Thanks.
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Old 08-14-2009, 03:26 AM   #92
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Quote:
Originally Posted by lindseyjane View Post
Hello,

I would like to visualise some paired reads data using MapView. I have tried to use MVFmaker and choose the checkbox of Paired-end data. However, this checkbox is greyed out and I cannot select it.

I am using MapView version 3.4.1 under ubuntu, using mono, and it seems to work fine otherwise. Can anyone tell me how to create the MVF file for my paired reads? Thanks.
Paired reads data is only supported for SOAP format.
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Old 08-14-2009, 04:22 AM   #93
strob
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Is this table still up to date?

http://www.sanger.ac.uk/Users/lh3/NGSalnview.shtml
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Old 08-25-2009, 09:53 AM   #94
yina
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Hi,

Mapview is a wonderfull tool, but i was wondering, is it possible to visualize, in a single file, the frequency of each base of all the positions in the reference??
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Old 09-17-2009, 03:18 AM   #95
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Default unrar problem?

Hello,
I*downloaded mapview, I*can see the files in the archive using the ubuntu 9.04 archive manager, but impossible to extract the files... Is there a password? the archive manager does like if it extracts it but the the files are not there in the end. If using the terminal, that is what I*get:

~/Desktop$ unrar -x mapview.rar

unrar 0.0.1 Copyright (C) 2004 Ben Asselstine, Jeroen Dekkers


Extracting from /home/yvan/Desktop/mapview.rar

Extracting readme.txt Failed
Extracting MVFmaker_NewFormat.txt Failed
Extracting MapView.exe Failed
3 Failed

Did anybody already experienced that and has a solution ?

Thanks a lot,
Yvan

EDIT: original source of mapview was http://evolution.sysu.edu.cn/software/mapview.rar I*however COULD*extract the zipped version there: https://sites.google.com/site/wjwdav...attredirects=0

Last edited by yvan.wenger; 09-17-2009 at 03:22 AM.
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Old 02-01-2010, 01:53 PM   #96
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Is anyone found an answer to "System.OverflowException: Overflow error." while try to jump to the end of the chr. somewher around ~111,000,000 nc region. I have tried both 64 bit and 32 bit machine and the error appeared in both..

The detail exception spewed looks like the following. I removed few lines specific to working dir on my workstation....
==============================================================

See the end of this message for details on invoking
just-in-time (JIT) debugging instead of this dialog box.

************** Exception Text **************
System.OverflowException: Overflow error.
at System.Drawing.Graphics.CheckErrorStatus(Int32 status)
at System.Drawing.Graphics.FillRectangle(Brush brush, Single x, Single y, Single width, Single height)
at MapView.Form1.48joJTB35(Object , PaintEventArgs )
at System.Windows.Forms.Control.OnPaint(PaintEventArgs e)
at System.Windows.Forms.Control.PaintTransparentBackground(PaintEventArgs e, Rectangle rectangle, Region transparentRegion)
at System.Windows.Forms.Control.PaintBackground(PaintEventArgs e, Rectangle rectangle, Color backColor, Point scrollOffset)
at System.Windows.Forms.Control.PaintBackground(PaintEventArgs e, Rectangle rectangle)
at System.Windows.Forms.Control.OnPaintBackground(PaintEventArgs pevent)
at System.Windows.Forms.Control.PaintWithErrorHandling(PaintEventArgs e, Int16 layer, Boolean disposeEventArgs)
at System.Windows.Forms.Control.WmPaint(Message& m)
at System.Windows.Forms.Control.WndProc(Message& m)
at System.Windows.Forms.Label.WndProc(Message& m)
at System.Windows.Forms.Control.ControlNativeWindow.OnMessage(Message& m)
at System.Windows.Forms.Control.ControlNativeWindow.WndProc(Message& m)
at System.Windows.Forms.NativeWindow.Callback(IntPtr hWnd, Int32 msg, IntPtr wparam, IntPtr lparam)


************** Loaded Assemblies **************
mscorlib
Assembly Version: 2.0.0.0
Win32 Version: 2.0.50727.3603 (GDR.050727-3600)
CodeBase: file:///C:/WINDOWS/Microsoft.NET/Framework/v2.0.50727/mscorlib.dll
----------------------------------------
MapView
Assembly Version: 3.4.1.0
Win32 Version: 3.4.1.0
CodeBase: ----------------------------------------
System.Windows.Forms
Assembly Version: 2.0.0.0
Win32 Version: 2.0.50727.3053 (netfxsp.050727-3000)
----------------------------------------
System
Assembly Version: 2.0.0.0
Win32 Version: 2.0.50727.3053 (netfxsp.050727-3000)
----------------------------------------
System.Drawing
Assembly Version: 2.0.0.0
Win32 Version: 2.0.50727.3053 (netfxsp.050727-3000)
----------------------------------------
Accessibility
Assembly Version: 2.0.0.0
Win32 Version: 2.0.50727.3053 (netfxsp.050727-3000)
----------------------------------------

************** JIT Debugging **************
To enable just-in-time (JIT) debugging, the .config file for this
application or computer (machine.config) must have the
jitDebugging value set in the system.windows.forms section.
The application must also be compiled with debugging
enabled.

For example:

<configuration>
<system.windows.forms jitDebugging="true" />
</configuration>

When JIT debugging is enabled, any unhandled exception
will be sent to the JIT debugger registered on the computer
rather than be handled by this dialog box.
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Old 03-30-2011, 02:10 PM   #97
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Quote:
Originally Posted by lh3 View Post
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.
Hello,

I would like to view a bam file in MapView but do not how to transform it to MVF format. Could you let me know it this can be done? That would help a lot
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Old 10-25-2011, 08:31 AM   #98
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Is there a known work flow from Abyss to MapView ?
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Old 08-23-2013, 08:05 AM   #99
htetre
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Default Unable to download MapView

Hello,

I have ace files that I would like to view and came across your MapView Software as a solution. However, I am unable to get any of the links in above messages to download a the program?

Thanks
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Old 08-23-2013, 08:12 AM   #100
GenoMax
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Quote:
Originally Posted by htetre View Post
Hello,

I have ace files that I would like to view and came across your MapView Software as a solution. However, I am unable to get any of the links in above messages to download a the program?

Thanks
This link is working: http://evolution.sysu.edu.cn/software/mapview.rar

Tablet also supports ace files: http://bioinf.scri.ac.uk/tablet/
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