c6b3a109267bc4a933b2d5937270c8eedd070f45
angie
  Fri Oct 12 16:52:10 2012 -0700
Feature #6336 (redistribution of samtools + tabix + KNETFILE_HOOKS patches):I made a combined, pre-patched package on github:
https://github.com/AngieHinrichs/samtabix
and modified common.mk to autodetect the /hive installation and use samtabix
preferentially to separate installations of samtools and tabix.
linefile.c is keeping some patch-specific function aliases for backwards
compatibility with tabix.

diff --git src/inc/common.mk src/inc/common.mk
index 5d45e63..05e3880 100644
--- src/inc/common.mk
+++ src/inc/common.mk
@@ -43,87 +43,89 @@
       PNGLIB=/usr/lib/libpng.a
   endif
 endif
 ifeq (${PNGLIB},)
   PNGLIB=-lpng
 endif
 
 L+=${PNGLIB}
 HG_INC+=${PNGINCL}
 
 # 32-bit color enabled by default
 ifneq (${COLOR32},0)
     HG_DEFS+=-DCOLOR32
 endif
 
-# autodetect local installation of samtools:
-ifeq (${SAMDIR},)
-  SAMDIR = /hive/data/outside/samtools/samtools-0.1.18/${MACHTYPE}
-  ifneq ($(wildcard ${SAMDIR}),)
-     KNETFILE_HOOKS=1
+# autodetect UCSC installation of samtabix:
+ifeq (${SAMTABIXDIR},)
+    SAMTABIXDIR = /hive/data/outside/samtabix/${MACHTYPE}
+    ifneq ($(wildcard ${SAMTABIXDIR}),)
+        ifeq (${USE_SAMTABIX},)
+          USE_SAMTABIX=1
+        endif
   endif
 endif
-ifeq (${USE_BAM},)
-  ifneq ($(wildcard ${SAMDIR}),)
+
+# libsamtabix (samtools + tabix + Angie's KNETFILE_HOOKS extension to it): disabled by default
+ifeq (${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
 
-# As we do for bam/samtools, so do for tabix.  autodetect local installation:
-ifeq (${TABIXDIR},)
-  TABIXDIR = /hive/data/outside/tabix/tabix-0.2.5/${MACHTYPE}
-  ifneq ($(wildcard ${TABIXDIR}),)
-     KNETFILE_HOOKS=1
-  endif
-endif
-ifeq (${USE_TABIX},)
-  ifneq ($(wildcard ${TABIXDIR}),)
-     USE_TABIX=1
-  endif
-endif
-
 # libtabix and Angie's KNETFILE_HOOKS extension to it: disabled by default
 ifeq (${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)
 FULLWARN = $(shell uname -n)
 
 ifeq (${HG_WARN},)
   ifeq (${SYS},Darwin)
       HG_WARN = -Wall -Wno-unused-variable
       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 -Wimplicit -Wreturn-type