Null pointer in iter_stream.h

[singerj]

Dear all,

There seems to be an issue with the casting in iter_stream.h.

When applying the following patch:

--- seqan-seqan-v2.3.2/include/seqan/stream/iter_stream.h
+++ seqan-seqan-v2.3.2/include/seqan/stream/iter_stream.h
@@ -240,8 +240,9 @@
     {}
 
     Iter(TIStream & stream) :
-        streamBuf(static_cast<StreamBuffer<TValue> *>(stream.rdbuf()))
+        streamBuf(dynamic_cast<StreamBuffer<TValue> *>(stream.rdbuf()))
     {
+        printf("streamBuf: %p\n", streamBuf);
         stream.exceptions(std::ios_base::badbit);
     }
 

example
seqan/demos/tutorial/sam_and_bam_io/example1.cpp
will throw
streamBuf: (nil)

Best,
Jochen

[singerj]

By the way, I tested it using g++-5.2.0 and g++-6.2.0

[smehringer]

Hi @singerj,
we're sorry for answering so late but a lot of us are on vacation around this time.

Why do you need this patch?

Since StreamBuffer is a derived class of std::basic_istream, a dynamic_cast will always fail because you are "down casting", so a static_cast is the proper thing to do is it not?

[singerj]

Hi @smehringer,

thanks for the reply. The code changes from above are not meant to be a patch, but much rather should only show the problem.

If I use -fsanitize=undefined,float-cast-overflow,float-divide-by-zero as compiler options for gcc(5.2.0/6.2.0) I get the following results on the original code:

seqan/2.1.1/include/seqan/stream/iter_stream.h:243:19: runtime error: downcast of address 0x7ffcbadd1198 which does not point to an object of type 'StreamBuffer'
0x7ffcbadd1198: note: object is of type 'std::basic_filebuf<char, std::char_traits<char> >'
 3a 7f 00 00  f8 00 5f 44 3a 7f 00 00  80 60 1b 01 00 00 00 00  80 60 1b 01 00 00 00 00  80 60 1b 01
              ^~~~~~~~~~~~~~~~~~~~~~~
              vptr for 'std::basic_filebuf<char, std::char_traits<char> >'
seqan/2.1.1/include/seqan/stream/iter_stream.h:295:19: runtime error: downcast of address 0x7f3a445f6880 which does not point to an object of type 'StreamBuffer'
0x7f3a445f6880: note: object is of type '__gnu_cxx::stdio_sync_filebuf<char, std::char_traits<char> >'
 00 00 00 00  38 fe 5e 44 3a 7f 00 00  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  00 00 00 00
              ^~~~~~~~~~~~~~~~~~~~~~~
              vptr for '__gnu_cxx::stdio_sync_filebuf<char, std::char_traits<char> >'
seqan/2.1.1/include/seqan/stream/iter_stream.h:662:5: runtime error: member call on address 0x7ffcbadd1198 which does not point to an object of type 'StreamBuffer'
0x7ffcbadd1198: note: object is of type 'std::basic_filebuf<char, std::char_traits<char> >'
 3a 7f 00 00  f8 00 5f 44 3a 7f 00 00  80 60 1b 01 00 00 00 00  84 60 1b 01 00 00 00 00  eb 61 1b 01
              ^~~~~~~~~~~~~~~~~~~~~~~
              vptr for 'std::basic_filebuf<char, std::char_traits<char> >'
seqan/2.1.1/include/seqan/stream/iter_stream.h:136:32: runtime error: member call on address 0x7ffcbadd1198 which does not point to an object of type 'StreamBuffer'
0x7ffcbadd1198: note: object is of type 'std::basic_filebuf<char, std::char_traits<char> >'
 3a 7f 00 00  f8 00 5f 44 3a 7f 00 00  80 60 1b 01 00 00 00 00  84 60 1b 01 00 00 00 00  eb 61 1b 01
              ^~~~~~~~~~~~~~~~~~~~~~~
              vptr for 'std::basic_filebuf<char, std::char_traits<char> >'
seqan/2.1.1/include/seqan/stream/iter_stream.h:139:13: runtime error: member call on address 0x7ffcbadd1198 which does not point to an object of type 'StreamBuffer'
0x7ffcbadd1198: note: object is of type 'std::basic_filebuf<char, std::char_traits<char> >'
 3a 7f 00 00  f8 00 5f 44 3a 7f 00 00  80 60 1b 01 00 00 00 00  84 60 1b 01 00 00 00 00  eb 61 1b 01
              ^~~~~~~~~~~~~~~~~~~~~~~
              vptr for 'std::basic_filebuf<char, std::char_traits<char> >'
seqan/2.1.1/include/seqan/stream/iter_stream.h:514:5: runtime error: member call on address 0x7f3a445f6880 which does not point to an object of type 'StreamBuffer'
0x7f3a445f6880: note: object is of type '__gnu_cxx::stdio_sync_filebuf<char, std::char_traits<char> >'
 00 00 00 00  38 fe 5e 44 3a 7f 00 00  00 00 00 00 00 00 00 00  00 00 00 00 00 00 00 00  00 00 00 00
              ^~~~~~~~~~~~~~~~~~~~~~~
              vptr for '__gnu_cxx::stdio_sync_filebuf<char, std::char_traits<char> >'
@HD	VN:1.3	SO:coordinate
@SQ	SN:ref	LN:45
@SQ	SN:ref2	LN:40
r001	163	ref	7	30	8M4I4M1D3M	=	37	39	TTAGATAAAGAGGATACTG	*	XX:B:S,12561,2,20,112
r002	0	ref	9	30	1S2I6M1P1I1P1I4M2I	*	0	0	AAAAGATAAGGGATAAA	*
r003	0	ref	9	30	5H6M	*	0	0	AGCTAA	*
r004	0	ref	16	30	6M14N1I5M	*	0	0	ATAGCTCTCAGC	*
r003	16	ref	29	30	6H5M	*	0	0	TAGGC	*
r001	83	ref	37	30	9M	=	7	-39	CAGCGCCAT	*

Note that this problem is also present in seqan2.3.2 and most likely in the develop branch as there are no code changes for the involved data types.

[singerj]

Hi @smehringer,

are there any news?

Cheers,
Jochen

[h-2]

Hey Jochen,

yeah, looks like something is broken. @temehi can you have a look at this? @rrahn will be coordinating another release of SeqAn2 in September, but right now many people are unavailable...

Best,
Hannes

[SoapGentoo]

@smehringer dynamic_cast is a superset of static_cast, and whenever static_cast is valid, so is dynamic_cast.