Run configure with the correct CC/CFLAGS/LDFLAGS env vars
Run configure with the correct CC/CFLAGS/LDFLAGS env vars

Ensure that configure uses the same compiler and CFLAGS/etc that
will be used later when the Cython and C source itself is compiled.

In particular, the sysconfig $CFLAGS (oddly enough) prevents the
compiler from searching /usr/local/include (at least on macOS).
Previously, configure sees /usr/local/include/lzma.h so defines
HAVE_LZMA_H; later when compiling htslib/cram/cram_io.c that
directory is not searched, leading to <lzma.h> not found errors.
Ensuring that configure also does not see lzma.h there leaves
HAVE_LZMA_H undefined, which activates HTSlib's os/lzma_stub.h
workaround for this header being missing.

Fixes #495. Fixes #828.

pysam-developers/pysam,pysam-developers/pysam,pysam-developers/pysam,pysam-developers/pysam