Similarly to the realloc(pac,...) within add1(), only bother to call
realloc() if appending the reverse complemented sequence requires more
space than is currently in the pac/m_pac buffer.
Avoids realloc(pac,0) (and a "Failed to allocate 0 bytes at bntseq.c"
message from wrap_realloc()) in the corner case of an empty reference
FASTA file. Fixes#54.
This function causes all kinds of problems when the reference genome consists
of many short reads/contigs/chromsomes. Some of the problems are nearly
unfixable at the point where bwa_fix_xref() gets called. This commit attempts
to fix the problem at the root. It disallows chains spanning multiple contigs
and never retrieves sequences bridging two adjacent contigs. Thus all the
chaining, extension, SW and global alignments are confined to on contig only.
This commit brings many changes. I have tested it on a couple examples
including Peter Field's PacBio example. It works well so far.
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.
Added a new utils.c wrapper err_gzclose and changed gzclose calls to use it.
Put in some more err_fflush calls before files being written are closed.
Made err_fflush call fsync. This is useful for remote filesystems where
errors may not be reported on fflush or fclose as problems at the server
end may only be detected after they have returned. If bwa is being used
only to write to local filesystems, calling fsync is not really necessary.
To disable it, comment out #define FSYNC_ON_FLUSH in utils.c.
zzh
Heng Li
John Marshall
Rob Davies
Heng Li