Nondeterministic segfault on OSX

[ljyanesm]

Example that segfaults:

(lldb) run --no-update-check /Volumes/yanesl-1/tophat2_accepted.bam
Process 92926 launched: '/Users/yanesl/workspace/cufflinks-2.2.1/cufflinks_build/cufflinks' (x86_64)
[14:56:57] Inspecting reads and determining fragment length distribution.
cufflinks was compiled with optimization - stepping may behave oddly; variables may not be available.
Process 92926 stopped
* thread #1, queue = 'com.apple.main-thread', stop reason = EXC_BAD_ACCESS (code=1, address=0x11e00000010)
    frame #0: 0x00000001000a6f20 cufflinks`BundleFactory::next_valid_alignment(ReadHit const*&) [inlined] boost::shared_ptr<Scaffold>::operator->(this=0x0000011e00000010) const at shared_ptr.hpp:735:16 [opt]
   732      typename boost::detail::sp_member_access< T >::type operator-> () const BOOST_SP_NOEXCEPT_WITH_ASSERT
   733      {
   734          BOOST_ASSERT( px != 0 );
-> 735          return px;
   736      }
   737
   738      typename boost::detail::sp_array_access< T >::type operator[] ( std::ptrdiff_t i ) const BOOST_SP_NOEXCEPT_WITH_ASSERT

Working example:

(lldb) run --no-update-check /Volumes/yanesl-1/tophat2_accepted.bam
Process 83429 launched: '/Users/yanesl/workspace/cufflinks-2.2.1/cufflinks_build/cufflinks' (x86_64)
[14:52:47] Inspecting reads and determining fragment length distribution.
> Processed 3306 loci.                         [*************************] 100%
Warning: Using default Gaussian distribution due to insufficient paired-end reads in open ranges.  It is recommended that correct parameters (--frag-len-mean and --frag-len-std-dev) be provided.
> Map Properties:
>   Normalized Map Mass: 22159.25
>   Raw Map Mass: 22159.25
>   Fragment Length Distribution: Truncated Gaussian (default)
>                 Default Mean: 200
>              Default Std Dev: 80
[14:52:49] Assembling transcripts and estimating abundances.
> Processing Locus Chr4:349181-349370          [                         ]   0%Process 83429 stopped
* thread #1, queue = 'com.apple.main-thread', stop reason = signal SIGSTOP
    frame #0: 0x00007fff647a486a libsystem_kernel.dylib`__psynch_cvwait + 10
libsystem_kernel.dylib`__psynch_cvwait:
->  0x7fff647a486a <+10>: jae    0x7fff647a4874            ; <+20>
    0x7fff647a486c <+12>: movq   %rax, %rdi
    0x7fff647a486f <+15>: jmp    0x7fff647a1457            ; cerror_nocancel
    0x7fff647a4874 <+20>: retq
Target 0: (cufflinks) stopped.

Both were run on the same machine and same build, just within minutes of each other.

Thanks for having a look.