[cdf]

Special thanks to Cristian!
MapView 3.4.0 Beta3 is running on Linux (Ubuntu 9.04) successfully.
After some changes and tests, I will release MapView 3.4.0 asap.

You're welcome!

I wait for the new version to test it!

Best regards,
Cristian

[WJW-Davy]

MapView 3.4.0
Download: https://sites.google.com/site/wjwdav...attredirects=0

3.4.0 [2009.6.1]
Run on Linux (e.g. Ubuntu 9) successfully.
Some bugs were fixed.

[fabio.marroni]

I am using MapView 3.4.0 on Ubuntu 9.04 using mono. It runs fine for almost everything, but as soon I try to run the coverage analysis (Statistics->Coverage Distribution) the program crashes with the following message:

  Unhandled Exception: System.IndexOutOfRangeException: Array index is out of range.
  at System.Windows.Forms.ListView.GetItemLocation (Int32 index) [0x00000] 
  at System.Windows.Forms.ListView.get_LastVisibleIndex () [0x00000] 
  at (wrapper remoting-invoke-with-check) System.Windows.Forms.ListView:get_LastVisibleIndex ()
  at System.Windows.Forms.ThemeWin32Classic.DrawListViewItems (System.Drawing.Graphics dc, Rectangle clip, System.Windows.Forms.ListView control) [0x00000] 
  at System.Windows.Forms.ListView+ItemControl.OnPaintInternal (System.Windows.Forms.PaintEventArgs pe) [0x00000] 
  at System.Windows.Forms.Control.WmPaint (System.Windows.Forms.Message& m) [0x00000] 
  at System.Windows.Forms.Control.WndProc (System.Windows.Forms.Message& m) [0x00000] 
  at System.Windows.Forms.ListView+ItemControl.WndProc (System.Windows.Forms.Message& m) [0x00000] 
  at System.Windows.Forms.Control+ControlWindowTarget.OnMessage (System.Windows.Forms.Message& m) [0x00000] 
  at System.Windows.Forms.Control+ControlNativeWindow.WndProc (System.Windows.Forms.Message& m) [0x00000] 
  at System.Windows.Forms.NativeWindow.WndProc (IntPtr hWnd, Msg msg, IntPtr wParam, IntPtr lParam) [0x00000] 
  at System.Windows.Forms.XplatUIX11.DispatchMessage (System.Windows.Forms.MSG& msg) [0x00000] 
  at System.Windows.Forms.XplatUI.DispatchMessage (System.Windows.Forms.MSG& msg) [0x00000] 
  at System.Windows.Forms.Application.RunLoop (Boolean Modal, System.Windows.Forms.ApplicationContext context) [0x00000] 
  at System.Windows.Forms.Application.Run (System.Windows.Forms.ApplicationContext context) [0x00000] 
  at System.Windows.Forms.Application.Run (System.Windows.Forms.Form mainForm) [0x00000] 
  at bQ9Wqc5Z49HhsqC7GB.VjrqIScir9R7qjLxc1.kAuOsLUbQ (System.String[] ) [0x00000]

Can you help with this issue?
Thank you very much
Fabio

[mikyatope]

I got this error with mono and MapView in a CentOS5

Unhandled Exception: System.TypeInitializationException: An exception was thrown by the type initializer for System.Windows.Forms.XplatUI ---> System.TypeInitializationException: An exception was thrown by the type initializer for System.Drawing.GDIPlus ---> System.DllNotFoundException: gdiplus.dll
  at (wrapper managed-to-native) System.Drawing.GDIPlus:GdiplusStartup (ulong&,System.Drawing.GdiplusStartupInput&,System.Drawing.GdiplusStartupOutput&)
  at System.Drawing.GDIPlus..cctor () [0x00000] --- End of inner exception stack trace ---

  at <0x00000> <unknown method>
  at System.Drawing.Graphics.FromHdcInternal (IntPtr hdc) [0x00000] 
  at System.Windows.Forms.XplatUIX11.SetDisplay (IntPtr display_handle) [0x00000] 
  at System.Windows.Forms.XplatUIX11..ctor () [0x00000] 
  at System.Windows.Forms.XplatUIX11.GetInstance () [0x00000] 
  at System.Windows.Forms.XplatUI..cctor () [0x00000] --- End of inner exception stack trace ---

  at <0x00000> <unknown method>
  at System.Windows.Forms.Application.EnableVisualStyles () [0x00000] 
  at bQ9Wqc5Z49HhsqC7GB.VjrqIScir9R7qjLxc1.kAuOsLUbQ (System.String[] ) [0x00000]

its a mono or a mapview issue ?
thanks!

[WJW-Davy]

I got this error with mono and MapView in a CentOS5

Unhandled Exception: System.TypeInitializationException: An exception was thrown by the type initializer for System.Windows.Forms.XplatUI ---> System.TypeInitializationException: An exception was thrown by the type initializer for System.Drawing.GDIPlus ---> System.DllNotFoundException: gdiplus.dll
  at (wrapper managed-to-native) System.Drawing.GDIPlus:GdiplusStartup (ulong&,System.Drawing.GdiplusStartupInput&,System.Drawing.GdiplusStartupOutput&)
  at System.Drawing.GDIPlus..cctor () [0x00000] --- End of inner exception stack trace ---

  at <0x00000> <unknown method>
  at System.Drawing.Graphics.FromHdcInternal (IntPtr hdc) [0x00000] 
  at System.Windows.Forms.XplatUIX11.SetDisplay (IntPtr display_handle) [0x00000] 
  at System.Windows.Forms.XplatUIX11..ctor () [0x00000] 
  at System.Windows.Forms.XplatUIX11.GetInstance () [0x00000] 
  at System.Windows.Forms.XplatUI..cctor () [0x00000] --- End of inner exception stack trace ---

  at <0x00000> <unknown method>
  at System.Windows.Forms.Application.EnableVisualStyles () [0x00000] 
  at bQ9Wqc5Z49HhsqC7GB.VjrqIScir9R7qjLxc1.kAuOsLUbQ (System.String[] ) [0x00000]

its a mono or a mapview issue ?
thanks!

The important part:
System.Drawing.GDIPlus ---> System.DllNotFoundException: gdiplus.dll
at (wrapper managed-to-native) System.Drawing.GDIPlus:GdiplusStartup (ulong&,System.Drawing.GdiplusStartupInput&,System.Drawing.GdiplusStartupOutput&)

I think your system or mono need GDIPlus.

[mikyatope]

^ Indeed, it was GDIplus , thanks !

[WJW-Davy]

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.

[WJW-Davy]

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.

[habm]

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!

[baohua100]

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.

[WJW-Davy]

Mono on Ubuntu

Mono on Ubuntu:

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

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

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:

mono Desktop/MapView.exe

[fabio.marroni]

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

[WJW-Davy]

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.

[hard998]

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:

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

  <2>  2009-6-30 16:02:46 
No SNP results!

[baohua100]

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:

  <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!