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License: GNU General Public License v2.0
Automatically exported from code.google.com/p/gbfp
License: GNU General Public License v2.0
What steps will reproduce the problem?
The parser segfaults whenever it encounters a feature like the following:
promoter <1..(1579.1736)
gdb says:
Program received signal SIGSEGV, Segmentation fault.
0x00007fa17f541265 in parseLocation (sLocation=<value optimized out>,
pFeature=0x28e3c40) at gbfp.c:402
402 pFeature->lEnd = ((pFeature->ptLocation)+(iLocationNum - 1))->lEnd;
What version of the product are you using? On what operating system?
gbfp 0.6.1
linux amd64
Please provide any additional information below.
Found the error while parsing the RefSeq record for NM_006517.
Original issue reported on code.google.com by [email protected]
on 3 Mar 2009 at 3:09
What steps will reproduce the problem?
1. Download and unpack http://gbfp.googlecode.com/files/gbfp-0.6.1.tgz
2. cd gbfp
3. make
What is the expected output? What do you see instead?
Expect gcc to work. Get:
$ make
gcc -O2 -Wall -ansi -pedantic -D_GNU_SOURCE -fPIC -g -c gbfp.c
gcc -shared -Wl,-h,libgbfp.so.0 -o libgbfp.so.0.6.1 gbfp.o
ld: unknown option: -h
collect2: ld returned 1 exit status
make: *** [libgbfp.so] Error 1
What version of the product are you using? On what operating system?
gbfp-0.6.1 on Mac OS X 10.6.5 (Snow Leopard)
Please provide any additional information below.
Original issue reported on code.google.com by [email protected]
on 6 Dec 2010 at 3:07
What steps will reproduce the problem?
1. installing package as a normal user with all permision
2.
3.
What is the expected output? What do you see instead?
to install python package easily
What version of the product are you using? On what operating system?
0.6.1
Please provide any additional information below.
Seems, in installation part your script try to access "/usr/local" which a
normal user in a network doesn't have access. It would be great if you could
patch it !
Original issue reported on code.google.com by [email protected]
on 2 Sep 2011 at 2:50
[deleted issue]
What steps will reproduce the problem?
1. Download a genome review file from (EMBL-Format):
http://www.ebi.ac.uk/GenomeReviews/files/cellular/
2. Convert it to GenBank, here:
http://www.ebi.ac.uk/cgi-bin/readseq.cgi
3. Parsing this file will return "Invalid Locus Line".
What version of the product are you using? On what operating system?
0.6.1
Please provide any additional information below.
would be great to let me know, if you find a temporary workaround
Files:
CP001742_GR.dat is the Genome Review file.
readseq.cgi is the converted GenBank file.
Original issue reported on code.google.com by [email protected]
on 2 Nov 2010 at 1:48
Attachments:
What steps will reproduce the problem?
1. running on a flat file such as the nc1213.flat from a daily incremental
update file
2. printing out the sGI field.
What is the expected output? What do you see instead?
The GI of each field should be printed. Instead you get "ION D" (for me, I
think that it is reading from the wrong part of memory, so this is probably not
reproducible.
What version of the product are you using? On what operating system?
0.6.1 on ubuntu 14.04
Please provide any additional information below.
The patch that fixes it for me is:
########################################
--- a/gbfp.c
+++ b/gbfp.c
@@ -227,16 +227,21 @@ static void parseAccession(FILE *FSeqFile, gb_data
*ptGBData) {
}
static void parseVersion(FILE *FSeqFile, gb_data *ptGBData) {
+ char prev;
+ int offset;
char sLine[LINELEN];
regmatch_t ptRegMatch[2];
getLine_w_rtrim(sLine, FSeqFile);
if (regexec(&ptRegExVersion, sLine, 2, ptRegMatch, 0) == 0) {
- *(sLine + ptRegMatch[1].rm_eo) = '\0';
+ offset = ptRegMatch[1].rm_eo;
+ prev = sLine[offset];
+ sLine[offset] = '\0';
ptGBData->sVersion = strdup(sLine + ptRegMatch[1].rm_so);
+ sLine[offset] = prev;
}
- if (regexec(&ptRegExGI, sLine + ptRegMatch[1].rm_eo + 1, 2, ptRegMatch, 0)
== 0) {
+ if (regexec(&ptRegExGI, sLine, 2, ptRegMatch, 0) == 0) {
*(sLine + ptRegMatch[1].rm_eo) = '\0';
ptGBData->sGI = strdup(sLine + ptRegMatch[1].rm_so);
}
Original issue reported on code.google.com by [email protected]
on 14 Jan 2015 at 2:56
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