Hi, I was looking for a program wich extracts bases from a bam file and compares it with the reference genome in the fasta format, using many options and i found Popbam : http://popbam.sourceforge.net/.
I compiled all the libraries and i ran the program with "popbam snp file.bam -f file.fasta", but after few seconds the message "segmentation fault" appears.
I don't know about this tools but in general make sure that all the data are in the right formats, the bam files are sorted and indexed (if that is required) the fasta file has the same sequence ids as the bam file, the fasta file is indexed (if that's required) etc.
In general its very hard to find out the reason for segmentation fault, unless you look know of the source code yourself or have the patience to understand it. A segmentation fault normally happens when the executable/code accesses a memory location that it has not reserved/doesn't have access to. So, the kernel says "nope".
However, normally in these cases, you could 1) Make sure you compiled it with right parameters for the right system 2) In case its written in C/C++, try to compile on another version of GCC/G++ (if they recommend a version, use that compiler). 3) Try compiling and running on another machine with different version of GCC/G++ and/or OS. Of course the last is 4) to write to the developers (or their forum) about the issue giving information about your machine, configuration, GCC/G++ version, compilation parameters, etc.. and how they can reproduce the issue and hope they respond! :)
I don't know about this tools but in general make sure that all the data are in the right formats, the bam files are sorted and indexed (if that is required) the fasta file has the same sequence ids as the bam file, the fasta file is indexed (if that's required) etc.