Just as we set r.failed and return early if there are no high-quality
read pairs at all, also do so if there are none within the calculated
boundaries. This avoids returning avg=NAN std=NAN, which leads to
malloc(INFINITY) and a crash; fixes#108.
In the bwa.c and bwase.c calls, rlen is an int64_t returned from
bns_get_seq() and is the number of reference bases covered by the
alignment; l_query/len is an int and the query length of the alignment;
and the result is an int given to an int parameter of ksw_global[2]().
As even the result is int and as rlen is effectively bounded by the
maximum length of a reference sequence, we maintain the status quo in
this code and simply cast rlen to int to silence Clang's "use llabs()"
(llabs() would not be a great answer given an int64_t anyway).
The bwtsw2_pair.c call needs to remain fabs() so both divisions are
done in floating point; cast to double to prevent Clang suggesting
changing the call to integer abs().
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.
1. Removed bwa.{h,c}. I am not going to finish them anyway.
2. Updated to the latest khash.h, which should be faster.
3. Define 64-bit vector and 128-bit integer/vector in utils.h.
Heng Li
John Marshall
Rob Davies
Heng Li