e327f01b1a1919b6441797f4757d55d317bddf1c
braney
  Wed Aug 31 17:17:55 2016 -0700
some small tweaks in htslib to better incorporate it in the build

diff --git src/htslib/Makefile src/htslib/Makefile
index 9692256..ea5ab04 100644
--- src/htslib/Makefile
+++ src/htslib/Makefile
@@ -10,37 +10,39 @@
 # to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 # copies of the Software, and to permit persons to whom the Software is
 # furnished to do so, subject to the following conditions:
 #
 # The above copyright notice and this permission notice shall be included in
 # all copies or substantial portions of the Software.
 #
 # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
 # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 # DEALINGS IN THE SOFTWARE.
 
-CC     = gcc
+kentSrc = ..
+include ${kentSrc}/inc/common.mk
+#CC     = gcc -p
 AR     = ar
 RANLIB = ranlib
 
 CPPFLAGS =
 # TODO: probably update cram code to make it compile cleanly with -Wc++-compat
-CFLAGS   = -ggdb -Wall -DKNETFILE_HOOKS -DUCSC_CRAM
+CFLAGS   += -DKNETFILE_HOOKS -DUCSC_CRAM
 EXTRA_CFLAGS_PIC = -fpic
 LDFLAGS  =
 LIBS     =
 
 # For now these don't work too well as samtools also needs to know to
 # add -lbz2 and -llzma if linking against the static libhts.a library.
 # TODO This needs configury and adding to htslib.pc.in.
 #
 # # Bzip2 support; optionally used by CRAM.
 # HAVE_LIBBZ2 := $(shell echo -e "\#include <bzlib.h>\012int main(void){return 0;}" > .test.c && $(CC) $(CFLAGS) $(CPPFLAGS) -o .test .test.c -lbz2 2>/dev/null && echo yes)
 # ifeq "$(HAVE_LIBBZ2)" "yes"
 # CPPFLAGS += -DHAVE_LIBBZ2
 # LIBS     += -lbz2
 # endif
 #