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segfault on osx #1

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brantfaircloth opened this Issue · 4 comments

2 participants

@brantfaircloth

hi there,

i was running into a segfault on osx using somewhat non-standard adapters (nextera adapter). the backtrace:

#0  0x00007fff80def32e in __strncat_chk ()
#1  0x00000001000034b3 in __inline_strncat_chk (__dest=0x1001004a0 "nextera_3_prime ", __src=0x0, __len=1) at _string.h:139
#2  0x0000000100003325 in load_adapters (fp=0x100100080) at src/util.c:46
#3  0x0000000100002157 in main (argc=4, argv=0x7fff5fbff438) at src/scythe.c:199

sent me to the adapters.fasta file i was using, the headers within which contained underscores, and the underscores appear to have caused the segfault. i've fixed my own problem by modifying the fasta header for the adapters, but it thought it might be useful to note the issue.

btw, scythe is a slick little program ; )

best,
b

@vsbuffalo vsbuffalo was assigned
@vsbuffalo
Owner

Hi Brant,

Thanks for reporting this. I believe I've taken care of this (April 12th commit) - could you let me know the commit you're on (first hash in git log)?

Vince

@vsbuffalo
Owner

Hi Brant,

Nevermind, I have reproduced your segfault on the newest version. I will fix this ASAP.

Thanks,
Vince

@brantfaircloth
@vsbuffalo
Owner

Hi Brant,

This issue should be fixed now. Can you let me know if the latest commit still segfaults?

I use Heng Li's excellent khash.h, which divides the header into name and comment fields, delimited by a space. My code concatenate these into a single header. However if there isn't a space, the old code would segfault.

Thanks again for reporting this!
Vince

@vsbuffalo vsbuffalo closed this
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