commandParser.parserFile() Isn't Resizing words Buffer Properly Leading To Seg Fault

[jgaupp-accuragen]

When running a 9 token command from a text file, I get a segment fault. The same command can be run from the command line and an equivalent 8 token command can be run from both a text file and the command line.

For example this 8 token command can be run from a file -

write 
test.wig 
sum 
FQ001_R1_S00000002.confirmedcounts.bw 
FQ000_R1_S00000000.confirmedcounts.bw 
FQ001_R1_S00000001.confirmedcounts.bw 
FQ001_R1_S00000000.confirmedcounts.bw 
FQ000_R1_S00000002.confirmedcounts.bw

While this 9 token command cannot -

write 
test.wig 
sum 
FQ001_R1_S00000002.confirmedcounts.bw 
FQ000_R1_S00000000.confirmedcounts.bw 
FQ001_R1_S00000001.confirmedcounts.bw 
FQ001_R1_S00000000.confirmedcounts.bw 
FQ000_R1_S00000002.confirmedcounts.bw
FQ000_R1_S00000001.confirmedcounts.bw

In commandParser.c, I replaced - words = realloc(words, arrayLength * sizeof(char)); with words = realloc(words, arrayLength * sizeof(char *));, recompiled and got a good file run with the 9 token command. I think that's the issue but if there's any misunderstanding, let me know.

Thanks for your work. I like the wiggletools syntax and based on small scale testing suspect it's going to offer a performance improvement over the toolset I'm currently using, particularly with respect to sort-free multi-file merge operations.

[dzerbino]

Hello @jgaupp-accuragen ,

Thanks a lot for the bug report, that was indeed a typo! I'm sending in a PR right now.

Cheers,

Daniel