Remove xmalloc, xcalloc, xrealloc and xstrdup from utils.h and revert calls
to the normal malloc, calloc, realloc, strdup. Add new files malloc_wrap.[ch]
with the wrapper functions. malloc_wrap.h #defines malloc etc. to the
wrapper, but only if USE_MALLOC_WRAPPERS has been defined.
Put #include "malloc_wrap.h" in any file that uses *alloc or strdup. This
is also in a #ifdef USE_MALLOC_WRAPPERS ... #endif block to make using the
wrappers optional. Add -DUSE_MALLOC_WRAPPERS into the makefile so they
should normally get added.
This is an improvement on the previous method as we now don't need to
worry about stray function calls that were not changed to the wrapped version
and the code will still work even if the wrapping is disabled.
Other possible methods of doing this are using malloc_hook (glibc-specific),
adding -include malloc_wrap.h to the gcc command-line (somewhat
gcc-specific) or making our own malloc function and using dlopen (scary).
This way is probably the most portable.
Released packages can be downloaded from SourceForge.net:
http://sourceforge.net/projects/bio-bwa/files/
Introduction and FAQ are available at:
http://bio-bwa.sourceforge.net
Manual page at:
http://bio-bwa.sourceforge.net/bwa.shtml
Mailing list:
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http://sourceforge.net/mail/?group_id=276243
Publications (Open Access):
http://www.ncbi.nlm.nih.gov/pubmed/20080505
http://www.ncbi.nlm.nih.gov/pubmed/19451168
Incomplete list of citations (via HubMed.org):
http://www.hubmed.org/references.cgi?uids=20080505
http://www.hubmed.org/references.cgi?uids=19451168
Related projects:
http://pbwa.sourceforge.net/
http://www.many-core.group.cam.ac.uk/projects/lam.shtml
http://biodoop-seal.sourceforge.net/
http://gitorious.org/bwa-cuda
96e445d9e4