11e45667d4e291b3038ccda729a1cdf5bcaf004a
braney
  Mon Jul 11 15:46:54 2016 -0700
incorporate htslib in kent src, remove USE_BAM, USE_SAMTABIX, USE_TABIX
defines, modify a bunch of makefiles to include kentSrc variable
pointing to top of the tree.

diff --git src/inc/common.mk src/inc/common.mk
index 9dc234d..1204208 100644
--- src/inc/common.mk
+++ src/inc/common.mk
@@ -5,39 +5,39 @@
 endif
 ifeq (${CFLAGS},)
     CFLAGS=
 endif
 ifeq (${MACHTYPE},)
     MACHTYPE:=$(shell uname -m)
 #    $(info MACHTYPE was empty, set to: ${MACHTYPE})
 endif
 ifneq (,$(findstring -,$(MACHTYPE)))
 #    $(info MACHTYPE has - sign ${MACHTYPE})
     MACHTYPE:=$(shell uname -m)
 #    $(info MACHTYPE has - sign set to: ${MACHTYPE})
 endif
 
 HG_DEFS=-D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -D_GNU_SOURCE -DMACHTYPE_${MACHTYPE}
-HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc
+HG_INC+=-I../inc -I../../inc -I../../../inc -I../../../../inc -I../../../../../inc -I$(kentSrc)/htslib
 
 # to check for Mac OSX Darwin specifics:
 UNAME_S := $(shell uname -s)
 # to check for builds on hgwdev
 FULLWARN = $(shell uname -n)
 
 #global external libraries 
-L=
+L=$(kentSrc)/htslib/libhts.a
 
 # pthreads is required
 ifneq ($(UNAME_S),Darwin)
   L+=-pthread
 endif
 
 # autodetect if openssl is installed
 ifeq (${SSLDIR},)
   SSLDIR = /usr/include/openssl
 endif
 ifeq (${USE_SSL},)
   ifneq ($(wildcard ${SSLDIR}),)
      USE_SSL=1
   endif
 endif
@@ -205,120 +205,42 @@
 # OK to add -lstdc++ to all MYSQLLIBS just in case it is
 #    MySQL version 5.6 libraries, but no 'librt' on Mac OSX
 ifeq (${FULLWARN},hgwdev)
   MYSQLLIBS += /usr/lib/gcc/x86_64-redhat-linux/4.4.4/libstdc++.a /usr/lib/debug/usr/lib64/librt.a
 else
   ifeq ($(UNAME_S),Darwin)
     MYSQLLIBS += -lstdc++
   else
     MYSQLLIBS += -lstdc++ -lrt
   endif
 endif
 
 L+=${PNGLIB}
 HG_INC+=${PNGINCL}
 
-# autodetect UCSC installation of htslib:
-ifeq (${HTSDIR},)
-    HTSDIR = /hive/data/outside/htslib/${MACHTYPE}
-    ifneq ($(wildcard ${HTSDIR}),)
-        ifeq (${USE_HTS},)
-            USE_HTS=1
-        endif
-    endif
-endif
-
-
-# autodetect UCSC installation of samtabix:
-ifeq (${SAMTABIXDIR},)
-    SAMTABIXDIR = /hive/data/outside/samtabix/${MACHTYPE}
-    ifneq ($(wildcard ${SAMTABIXDIR}),)
-        ifeq (${USE_SAMTABIX},)
-          USE_SAMTABIX=1
-        endif
-    endif
-endif
-
 # pass through COREDUMP
 ifneq (${COREDUMP},)
     HG_DEFS+=-DCOREDUMP
 endif
 
 # autodetect UCSC additional source code with password for some external tracks on gbib
 GBIBDIR = /hive/groups/browser/gbib/
 ifneq ($(wildcard ${GBIBDIR}/*.c),)
   HG_DEFS+=-DUSE_GBIB_PWD
   HG_INC += -I${GBIBDIR}
 endif
 
-ifeq (${USE_HTS},1)
-    HG_DEFS+=-DUSE_HTS
-    USE_SAMTABIX=1
-    SAMTABIXDIR = ${HTSDIR}
-    SAMTABIXLIB=${HTSDIR}/libhts.a
-endif
-
-# libsamtabix (samtools + tabix + Angie's KNETFILE_HOOKS extension to it): disabled by default
-ifeq (${USE_SAMTABIX},1)
-    KNETFILE_HOOKS=1
-    USE_BAM=1
-    USE_TABIX=1
-    ifeq (${SAMTABIXINC},)
-        SAMTABIXINC = ${SAMTABIXDIR}
-    endif
-    ifeq (${SAMTABIXLIB},)
-        SAMTABIXLIB = ${SAMTABIXDIR}/libsamtabix.a
-    endif
-    HG_INC += -I${SAMTABIXINC}
-    L+=${SAMTABIXLIB} -lz
-    HG_DEFS+=-DUSE_SAMTABIX -DUSE_BAM -DUSE_TABIX -DKNETFILE_HOOKS
-else
-  # Deprecated but supported for mirrors, for now: independent samtools and tabix libs
-
-  # libbam (samtools, and Angie's KNETFILE_HOOKS extension to it): disabled by default
-  ifeq (${USE_BAM},1)
-      ifeq (${SAMINC},)
-          SAMINC = ${SAMDIR}
-      endif
-      ifeq (${SAMLIB},)
-          SAMLIB = ${SAMDIR}/libbam.a
-      endif
-      HG_INC += -I${SAMINC}
-      L+=${SAMLIB}
-      HG_DEFS+=-DUSE_BAM
-      ifeq (${KNETFILE_HOOKS},1)
-          HG_DEFS+=-DKNETFILE_HOOKS
-      endif
-  endif
-
-  # libtabix and Angie's KNETFILE_HOOKS extension to it: disabled by default
-  ifeq (${USE_TABIX},1)
-      ifeq (${TABIXINC},)
-          TABIXINC = ${TABIXDIR}
-      endif
-      ifeq (${TABIXLIB},)
-          TABIXLIB = ${TABIXDIR}/libtabix.a
-      endif
-      HG_INC += -I${TABIXINC}
-      L+=${TABIXLIB} -lz
-      HG_DEFS+=-DUSE_TABIX
-      ifeq (${KNETFILE_HOOKS},1)
-	HG_DEFS+=-DKNETFILE_HOOKS
-      endif
-  endif
-endif
-
 SYS = $(shell uname -s)
 
 ifeq (${HG_WARN},)
   ifeq (${SYS},Darwin)
       HG_WARN = -Wall -Wno-unused-variable -Wno-deprecated-declarations
       HG_WARN_UNINIT=
   else
     ifeq (${SYS},SunOS)
       HG_WARN = -Wall -Wformat -Wimplicit -Wreturn-type
       HG_WARN_UNINIT=-Wuninitialized
     else
       ifeq (${FULLWARN},hgwdev)
         HG_WARN = -Wall -Werror -Wformat -Wformat-security -Wimplicit -Wreturn-type -Wempty-body -Wunused-but-set-variable
         HG_WARN_UNINIT=-Wuninitialized
       else