abiswas-odu / gbfp Goto Github PK

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.

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.

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 !

[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.

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);
     }