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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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Segmentation fault - burden test skato when run with option --outputRaw #59

Closed manu148 closed 5 years ago

manu148 commented 6 years ago

Hi, I am running skat-o burden test using ucsc refFlat file(b38). The program is crashing with segmentation fault. For some of the genes/bins the length of fn.c_str() is greater than 255. Since linux has a maximum filename length of 255 characters for most filesystems(including EXT4), the fDump is NULL and segmentation fault occurs in following lines. https://github.com/zhanxw/rvtests/blob/a6f79347c6eaf1a8fa7950a42a2be2df32747128/src/Model.h#L5155

Capping the max length if (fn.length() > 30) { fn = fn.substr(0, 30) + ".data"; } did solve my problem.

Thanks, Manu

zhanxw commented 5 years ago

Thanks for the tip. I will safe guard the length of file name.

bestmichaelbrown commented 5 years ago

Hi,

I believe I am having this problem too. I am running Burden tests and have no issues when I do not add --outputRaw, but including --outputRaw causes a Segmentation fault. Has this been fixed in version 20190128 (git: 65f00ac2b8a48b52ffae17b2e784dbc39211360d)?

zhanxw commented 5 years ago

Sorry, it is not fixed in 20180128. I will release a new version for that. Sorry for the inconvenience.

bestmichaelbrown commented 5 years ago

I tested the latest version and it seems to work just fine now. Thank you very much, I really appreciate it!