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GCLib - Genomic C++ library of reusable code for bioinformatics projects

License: Other

C++ 79.57% Makefile 0.35% C 20.05% Shell 0.03%

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xiongxu bowhan xuertowong ramatam bioinfoacademy bioinfotools whc2 christopherwilks lehmannn rob-p smoe adityashukl1502 alevar

gclib's Issues

add support for multiple codon tables

Originally posted by @Maarten-vd-Sande in gpertea/gffread#21 (comment)

Just dropping in to say that supporting multiple tables would be an awesome feature (for me). I haven't found any other tool that works as easy and fast as gffread.

Would you support a PR in this direction, if so, can you give some pointers? It's been over 5 years since I did anything serious with C++ so it might not result into anything useful though 😇 .. I can't seem to find where the table is defined..

gclib/codons.cpp

Line 7 in f6817ea

static char codonData[]={ //long list of 3+1 characters (codon+translation)

Uninitialized GFF line info causes out-of-bounds-read, possible out-of-bounds-write.

Reproduce

PoC Input: min.gz

Steps to Reproduce:

  1. Compile GffRead v0.12.7 (will fetch GCLib v0.12.7)
  2. Decompress PoC input: gzip -d min.gz
  3. Run: ./gffread -E min -o out

Output:

Command line was:
./gffread -E min -o out
Segmentation fault

Root Cause

gclib/gff.cpp

Lines 413 to 432 in 8aee376

while (line[i]!=0) {
if (line[i]=='\t') {
line[i]=0;
t[tidx]=line+i+1;
tidx++;
//if (tidx>8) break;
}
i++;
}
if (tidx<8) { // ignore non-GFF lines
return;
}
if (tidx>9) {
GMessage("Warning: unexpected tab character in last column, line truncated:\n\%s\n",l);
}
gffWarnings=reader->gff_warns;
gseqname=t[0];
track=t[1];
ftype=t[2];
info=t[8];

When GCLib reads a GFF line with no info segment, the char * at t[8] will not be set, causing it to take on whatever stale value happens to be in that location of the stack. Triggered accidentally, this can cause a segfault due to reading an invalid address here:

gclib/gff.cpp

Line 118 in 8aee376

while (notfound && *pos) {

However, a maliciously crafted input may be able to place a valid pointer at this location, causing a more severe vulnerability.

Proposed Patch

At a minimum, t should be zeroed during initialization:

*** v0.12.7/gclib/gff.cpp     2021-07-23 10:31:39.000000000 -0400
--- new/gclib/gff.cpp       2021-10-04 10:54:52.989309121 -0400
*************** GffLine::GffLine(GffReader* reader, cons
*** 405,411 ****
   GMALLOC(dupline, llen+1);
   memcpy(dupline, l, llen+1);
   skipLine=true; //clear only if we make it to the end of this function
!  char* t[9];
   int i=0;
   int tidx=1;
   t[0]=line;
--- 405,411 ----
   GMALLOC(dupline, llen+1);
   memcpy(dupline, l, llen+1);
   skipLine=true; //clear only if we make it to the end of this function
!  char* t[9] = {0};
   int i=0;
   int tidx=1;
   t[0]=line;

Ideally, the library should gracefully handle no info being found (this only works if t is zero initialized):

*** v0.12.7/gclib/gff.cpp     2021-07-23 10:31:39.000000000 -0400
--- new/gclib/gff.cpp       2021-10-04 10:54:52.989309121 -0400
*************** GffLine::GffLine(GffReader* reader, cons
*** 430,435 ****
--- 430,439 ----
   track=t[1];
   ftype=t[2];
   info=t[8];
+  if (!info) {
+    GMessage("Warning: missing info:\n%s\n",l);
+    return;
+  }
   char* p=t[3];
   if (!parseUInt(p,fstart)) {
     //chromosome_band entries in Flybase

Credit

This bug was detected using AFL and localized using ARCUS.

g++ warnings -

Hello,

Admittedly, I do not see any immediate need to address any of these warnings.

Kind regards,
Steffen

$ gcc --version
gcc (Debian 10.2.0-3) 10.2.0

libtool: compile:  g++ -DHAVE_CONFIG_H -I. -I. -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/home/moeller/git/med-team/libgclib=. -fstack-protector-strong -Wformat -Werror=format-security -Wall -pedantic -flto -fPIC -D_FILE_OFFSET_BITS=64 -c GStr.cpp  -fPIC -DPIC -o .libs/libgclib_la-GStr.o
In file included from gff.cpp:1:
gff.h:229:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  229 |      struct {
      |             ^
gff.h:232:13: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  232 |      struct {
      |             ^
gff.h:328:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  328 |     struct {
      |            ^
gff.h:691:14: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
  691 |       struct {
      |              ^
gff.h:1150:12: warning: ISO C++ prohibits anonymous structs [-Wpedantic]
 1150 |     struct {
      |            ^
In file included from GList.hh:8,
                 from GFastaIndex.h:12,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gff.cpp:1:
GVec.hh: In instantiation of ‘void GVec<OBJ>::setCapacity(int) [with OBJ = GMapSeg]’:
GVec.hh:202:3:   required from ‘GVec<OBJ>::GVec(int) [with OBJ = GMapSeg]’
gff.h:127:50:   required from here
GVec.hh:291:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GMapSeg’; use assignment or value-initialization instead [-Wclass-memaccess]
  291 |         memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.cpp:1:
gff.h:70:7: note: ‘class GMapSeg’ declared here
   70 | class GMapSeg:public GSeg {
      |       ^~~~~~~
In file included from GList.hh:8,
                 from GFastaIndex.h:12,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gff.cpp:1:
GVec.hh: In instantiation of ‘void GVec<OBJ>::setCapacity(int) [with OBJ = GSeg]’:
GVec.hh:202:3:   required from ‘GVec<OBJ>::GVec(int) [with OBJ = GSeg]’
gff.h:311:92:   required from here
GVec.hh:291:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; use assignment or value-initialization instead [-Wclass-memaccess]
  291 |         memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.h:6,
                 from gff.cpp:1:
GBase.h:308:7: note: ‘class GSeg’ declared here
  308 | class GSeg {
      |       ^~~~
In file included from GList.hh:8,
                 from GFastaIndex.h:12,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gff.cpp:1:
GVec.hh: In instantiation of ‘void GVec<OBJ>::setCapacity(int) [with OBJ = GeneCDS]’:
GVec.hh:202:3:   required from ‘GVec<OBJ>::GVec(int) [with OBJ = GeneCDS]’
gff.h:1351:31:   required from here
GVec.hh:291:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GeneCDS’; use assignment or value-initialization instead [-Wclass-memaccess]
  291 |         memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.cpp:1:
gff.h:1340:7: note: ‘class GeneCDS’ declared here
 1340 | class GeneCDS: public GSeg {
      |       ^~~~~~~
In file included from GList.hh:8,
                 from GFastaIndex.h:12,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gff.cpp:1:
GVec.hh: In instantiation of ‘void GVec<OBJ>::setCapacity(int) [with OBJ = GffExon]’:
GVec.hh:202:3:   required from ‘GVec<OBJ>::GVec(int) [with OBJ = GffExon]’
gff.cpp:2315:16:   required from here
GVec.hh:291:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GffExon’; use assignment or value-initialization instead [-Wclass-memaccess]
  291 |         memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.cpp:1:
gff.h:629:7: note: ‘class GffExon’ declared here
  629 | class GffExon : public GSeg {
      |       ^~~~~~~
In file included from GList.hh:8,
                 from GFastaIndex.h:12,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gff.cpp:1:
GVec.hh: In instantiation of ‘void GVec<OBJ>::setCapacity(int) [with OBJ = GSegMatch]’:
GVec.hh:202:3:   required from ‘GVec<OBJ>::GVec(int) [with OBJ = GSegMatch]’
GList.hh:191:76:   required from ‘GArray<OBJ>::GArray(int (*)(pointer, pointer)) [with OBJ = GSegMatch; GCompareProc = int(void*, void*); pointer = void*]’
gff.h:1351:31:   required from here
GVec.hh:291:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSegMatch’; use assignment or value-initialization instead [-Wclass-memaccess]
  291 |         memset(fArray+fCount, 0, (NewCapacity-fCount)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.cpp:1:
gff.h:1328:7: note: ‘class GSegMatch’ declared here
 1328 | class GSegMatch { //keep track of "matching" overlaps of a GeneCDSChain with multiple GeneSegment containers
      |       ^~~~~~~~~
In file included from GList.hh:8,
                 from GFastaIndex.h:12,
                 from GFaSeqGet.h:3,
                 from gff.h:9,
                 from gff.cpp:1:
GVec.hh: In instantiation of ‘void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GSegMatch]’:
GVec.hh:437:9:   required from ‘void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GSegMatch]’
GVec.hh:69:44:   required from ‘void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GSegMatch]’
GList.hh:234:21:   required from ‘int GArray<OBJ>::Add(OBJ*) [with OBJ = GSegMatch]’
GList.hh:51:36:   required from ‘int GArray<OBJ>::Add(OBJ&) [with OBJ = GSegMatch]’
gff.h:1364:22:   required from here
GVec.hh:358:15: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSegMatch’; use assignment or value-initialization instead [-Wclass-memaccess]
  358 |         memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ));
      |         ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from gff.cpp:1:
gff.h:1328:7: note: ‘class GSegMatch’ declared here
 1328 | class GSegMatch { //keep track of "matching" overlaps of a GeneCDSChain with multiple GeneSegment containers
      |       ^~~~~~~~~

tag a release

Can you please tag a release of this software? We'd like to user gffread and build it consistently with a tagged version of this lib. Tags are much nicer than using commit hashes...

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