[GenABEL-dev] [genabel-Bugs][4919] Too small reading buffers for long alleles in mach info and legend files

[Yury Aulchenko]

It is really great to see three people contributing to the fix of this bug! - bravi, Daniel, Xia, Lennart!

Yurii

On Nov 4, 2013, at 11:13 AM, <genabel-bugs at r-forge.r-project.org> <genabel-bugs at r-forge.r-project.org> wrote:

> Bugs item #4919, was changed at 2013-09-19 12:41 by Lennart Karssen
> You can respond by visiting: 
> https://r-forge.r-project.org/tracker/?func=detail&atid=2058&aid=4919&group_id=505
> 
>> Status: Closed
> Priority: 3
> Submitted By: Daniel Taliun (dtaliun)
> Assigned to: Lennart Karssen (lckarssen)
> Summary: Too small reading buffers for long alleles in mach info and legend files 
>> Resolution: Fixed
> Operating System: All
> Severity: trivial
> Hardware: All
> Version: PA v0.4.1
> Component: ProbABEL
> URL: 
> 
> 
> Initial Comment:
> 1) Segmentation fault when trying to read mach info file that contains alleles longer than 100 characters.
> The issue is too small buffer allocated in mlinfo::mlinfo(char * filename, char * mapname) : only 100 characters (data.cpp, line 72)
> 
> 2) The same problem is when reading map file (if --map option is specified). The buffer of 1000 characters is not enough and as a result position is always equal to -999 (data.cpp, line 139).
> 
> Generally insertion/deletion alleles can be extremely long. But buffer of 1MB (1048576 characters) should be enough and cost nothing.
> 
> ----------------------------------------------------------------------
> 
>> Comment By: Lennart Karssen (lckarssen)
> Date: 2013-11-04 11:13
> 
> Message:
> Fixed in SVN r.1360 with the patch provided by Daniel Taliun (patch #4936). 
> 
> 
> Thanks Daniel!
> Thanks to Xia Shen for testing the fix.
> 
> ----------------------------------------------------------------------
> 
> Comment By: Lennart Karssen (lckarssen)
> Date: 2013-09-19 13:04
> 
> Message:
> Thanks for the report Daniel, and for the suggested fix. 
> 
> ----------------------------------------------------------------------
> 
> You can respond by visiting: 
> https://r-forge.r-project.org/tracker/?func=detail&atid=2058&aid=4919&group_id=505