buffer overflow with demo

[karel-brinda]

~/github/MOSAIK/demo$ ./Align.sh 
------------------------------------------------------------------------------
MosaikAligner 2.2.30                                                2014-06-27
Wan-Ping Lee & Michael Stromberg  Marth Lab, Boston College Biology Department
------------------------------------------------------------------------------

WARNING: Paired-end data is detected, but the median fragment length is not specified.
         Accordingly, local alignment search is not enabled.
         The median fragment length (-mfl parameter) can be specified in MosaikBuild.

- Using the following alignment algorithm: all positions
- Using the following alignment mode: aligning reads to all possible locations
- Using a maximum mismatch percent threshold of 0.15
- Using a Smith-Waterman bandwidth of 39
- Using an alignment candidate threshold of 33bp.
- Setting hash position threshold to 200
- loading reference sequence... finished.

Hashing reference sequence:
100%[======================================================] 4,938,906 ref bases/s        in  1 s  


Aligning read library (5000):
 0% [                                                          ]                                  |
ERROR: buffer overflow detected when creating the packed cigar string.

[linolala]

Not sure if you're still fighting the same problem.
It's actually an issue with the latest Mosaik version and has been addressed earlier:

Reverting to v.2.2.26 seems to solve the problem:
git checkout e04c806; cd src; make clean; make
whereafter the demo works ok.