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/htslib/config.log src/htslib/config.log
new file mode 100644
index 0000000..ebd670d
--- /dev/null
+++ src/htslib/config.log
@@ -0,0 +1,418 @@
+This file contains any messages produced by compilers while
+running configure, to aid debugging if configure makes a mistake.
+
+It was created by HTSlib configure 1.3, which was
+generated by GNU Autoconf 2.69.  Invocation command line was
+
+  $ ./configure 
+
+## --------- ##
+## Platform. ##
+## --------- ##
+
+hostname = hgwdev
+uname -m = x86_64
+uname -r = 2.6.32-504.3.3.el6.x86_64
+uname -s = Linux
+uname -v = #1 SMP Wed Dec 17 01:55:02 UTC 2014
+
+/usr/bin/uname -p = unknown
+/bin/uname -X     = unknown
+
+/bin/arch              = x86_64
+/usr/bin/arch -k       = unknown
+/usr/convex/getsysinfo = unknown
+/usr/bin/hostinfo      = unknown
+/bin/machine           = unknown
+/usr/bin/oslevel       = unknown
+/bin/universe          = unknown
+
+PATH: /parasol/bin
+PATH: /parasol/bin
+PATH: /cluster/bin/x86_64
+PATH: /cluster/software/bin
+PATH: /parasol/bin
+PATH: /parasol/bin
+PATH: /cluster/bin/x86_64
+PATH: /cluster/software/bin
+PATH: /usr/lib64/qt-3.3/bin
+PATH: /usr/NX/bin
+PATH: /parasol/bin
+PATH: /parasol/bin
+PATH: /cluster/bin/x86_64
+PATH: /cluster/software/bin
+PATH: /usr/local/bin
+PATH: /bin
+PATH: /usr/bin
+PATH: /projects/linux/matlab/bin
+PATH: /cluster/bin/scripts
+PATH: /cluster/home/braney/bin/scripts
+PATH: /cluster/bin/scripts
+PATH: /cluster/home/braney/bin
+PATH: /cluster/bin/x86_64
+PATH: /cluster/home/braney/bin/x86_64
+PATH: /projects/compbio/bin
+PATH: /projects/compbio/bin/i686
+PATH: /hive/groups/recon/local/bin
+PATH: /usr/local/sbin
+PATH: /usr/sbin
+PATH: /sbin
+PATH: /usr/lpp/mmfs/bin/
+PATH: /opt/dell/srvadmin/bin
+PATH: /projects/linux/matlab/bin
+PATH: /cluster/bin/scripts
+PATH: /cluster/home/braney/bin/scripts
+PATH: /cluster/bin/scripts
+PATH: /cluster/home/braney/bin
+PATH: /cluster/bin/x86_64
+PATH: /cluster/home/braney/bin/x86_64
+PATH: /projects/compbio/bin
+PATH: /projects/compbio/bin/i686
+PATH: /hive/groups/recon/local/bin
+PATH: /cluster/home/braney/bin
+PATH: /projects/linux/matlab/bin
+PATH: /cluster/bin/scripts
+PATH: /cluster/home/braney/bin/scripts
+PATH: /cluster/bin/scripts
+PATH: /cluster/home/braney/bin
+PATH: /cluster/bin/x86_64
+PATH: /cluster/home/braney/bin/x86_64
+PATH: /projects/compbio/bin
+PATH: /projects/compbio/bin/i686
+PATH: /hive/groups/recon/local/bin
+
+
+## ----------- ##
+## Core tests. ##
+## ----------- ##
+
+configure:2091: checking for gcc
+configure:2118: result: gcc34
+configure:2347: checking for C compiler version
+configure:2356: gcc34 --version >&5
+gcc34 (GCC) 3.4.6 20060404 (Red Hat 3.4.6-19.el6)
+Copyright (C) 2006 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions.  There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
+
+configure:2367: $? = 0
+configure:2356: gcc34 -v >&5
+Reading specs from /usr/lib/gcc/x86_64-redhat-linux/3.4.6/specs
+Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --enable-shared --enable-threads=posix --disable-checking --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-languages=c,c++,f77 --disable-libgcj --host=x86_64-redhat-linux
+Thread model: posix
+gcc version 3.4.6 20060404 (Red Hat 3.4.6-19.el6)
+configure:2367: $? = 0
+configure:2356: gcc34 -V >&5
+gcc34: `-V' option must have argument
+configure:2367: $? = 1
+configure:2356: gcc34 -qversion >&5
+gcc34: unrecognized option `-qversion'
+gcc34: no input files
+configure:2367: $? = 1
+configure:2387: checking whether the C compiler works
+configure:2409: gcc34    conftest.c  >&5
+configure:2413: $? = 0
+configure:2461: result: yes
+configure:2464: checking for C compiler default output file name
+configure:2466: result: a.out
+configure:2472: checking for suffix of executables
+configure:2479: gcc34 -o conftest    conftest.c  >&5
+configure:2483: $? = 0
+configure:2505: result: 
+configure:2527: checking whether we are cross compiling
+configure:2535: gcc34 -o conftest    conftest.c  >&5
+configure:2539: $? = 0
+configure:2546: ./conftest
+configure:2550: $? = 0
+configure:2565: result: no
+configure:2570: checking for suffix of object files
+configure:2592: gcc34 -c   conftest.c >&5
+configure:2596: $? = 0
+configure:2617: result: o
+configure:2621: checking whether we are using the GNU C compiler
+configure:2640: gcc34 -c   conftest.c >&5
+configure:2640: $? = 0
+configure:2649: result: yes
+configure:2658: checking whether gcc34 accepts -g
+configure:2678: gcc34 -c -g  conftest.c >&5
+configure:2678: $? = 0
+configure:2719: result: yes
+configure:2736: checking for gcc34 option to accept ISO C89
+configure:2799: gcc34  -c -g -O2  conftest.c >&5
+configure:2799: $? = 0
+configure:2812: result: none needed
+configure:2875: checking for ranlib
+configure:2891: found /usr/bin/ranlib
+configure:2902: result: ranlib
+configure:2990: checking how to run the C preprocessor
+configure:3021: gcc34 -E  conftest.c
+configure:3021: $? = 0
+configure:3035: gcc34 -E  conftest.c
+conftest.c:9:28: ac_nonexistent.h: No such file or directory
+configure:3035: $? = 1
+configure: failed program was:
+| /* confdefs.h */
+| #define PACKAGE_NAME "HTSlib"
+| #define PACKAGE_TARNAME "htslib"
+| #define PACKAGE_VERSION "1.3"
+| #define PACKAGE_STRING "HTSlib 1.3"
+| #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net"
+| #define PACKAGE_URL "http://www.htslib.org/"
+| /* end confdefs.h.  */
+| #include <ac_nonexistent.h>
+configure:3060: result: gcc34 -E
+configure:3080: gcc34 -E  conftest.c
+configure:3080: $? = 0
+configure:3094: gcc34 -E  conftest.c
+conftest.c:9:28: ac_nonexistent.h: No such file or directory
+configure:3094: $? = 1
+configure: failed program was:
+| /* confdefs.h */
+| #define PACKAGE_NAME "HTSlib"
+| #define PACKAGE_TARNAME "htslib"
+| #define PACKAGE_VERSION "1.3"
+| #define PACKAGE_STRING "HTSlib 1.3"
+| #define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net"
+| #define PACKAGE_URL "http://www.htslib.org/"
+| /* end confdefs.h.  */
+| #include <ac_nonexistent.h>
+configure:3123: checking for grep that handles long lines and -e
+configure:3181: result: /bin/grep
+configure:3186: checking for egrep
+configure:3248: result: /bin/grep -E
+configure:3253: checking for ANSI C header files
+configure:3273: gcc34 -c -g -O2  conftest.c >&5
+configure:3273: $? = 0
+configure:3346: gcc34 -o conftest -g -O2   conftest.c  >&5
+configure:3346: $? = 0
+configure:3346: ./conftest
+configure:3346: $? = 0
+configure:3357: result: yes
+configure:3370: checking for sys/types.h
+configure:3370: gcc34 -c -g -O2  conftest.c >&5
+configure:3370: $? = 0
+configure:3370: result: yes
+configure:3370: checking for sys/stat.h
+configure:3370: gcc34 -c -g -O2  conftest.c >&5
+configure:3370: $? = 0
+configure:3370: result: yes
+configure:3370: checking for stdlib.h
+configure:3370: gcc34 -c -g -O2  conftest.c >&5
+configure:3370: $? = 0
+configure:3370: result: yes
+configure:3370: checking for string.h
+configure:3370: gcc34 -c -g -O2  conftest.c >&5
+configure:3370: $? = 0
+configure:3370: result: yes
+configure:3370: checking for memory.h
+configure:3370: gcc34 -c -g -O2  conftest.c >&5
+configure:3370: $? = 0
+configure:3370: result: yes
+configure:3370: checking for strings.h
+configure:3370: gcc34 -c -g -O2  conftest.c >&5
+configure:3370: $? = 0
+configure:3370: result: yes
+configure:3370: checking for inttypes.h
+configure:3370: gcc34 -c -g -O2  conftest.c >&5
+configure:3370: $? = 0
+configure:3370: result: yes
+configure:3370: checking for stdint.h
+configure:3370: gcc34 -c -g -O2  conftest.c >&5
+configure:3370: $? = 0
+configure:3370: result: yes
+configure:3370: checking for unistd.h
+configure:3370: gcc34 -c -g -O2  conftest.c >&5
+configure:3370: $? = 0
+configure:3370: result: yes
+configure:3388: checking for stdlib.h
+configure:3388: result: yes
+configure:3388: checking for unistd.h
+configure:3388: result: yes
+configure:3388: checking for sys/param.h
+configure:3388: gcc34 -c -g -O2  conftest.c >&5
+configure:3388: $? = 0
+configure:3388: result: yes
+configure:3408: checking for getpagesize
+configure:3408: gcc34 -o conftest -g -O2   conftest.c  >&5
+configure:3408: $? = 0
+configure:3408: result: yes
+configure:3417: checking for working mmap
+configure:3564: gcc34 -o conftest -g -O2   conftest.c  >&5
+configure:3564: $? = 0
+configure:3564: ./conftest
+configure:3564: $? = 0
+configure:3574: result: yes
+configure:3585: checking for gmtime_r
+configure:3585: gcc34 -o conftest -g -O2   conftest.c  >&5
+configure:3585: $? = 0
+configure:3585: result: yes
+configure:3666: checking for zlib.h
+configure:3666: gcc34 -c -g -O2  conftest.c >&5
+configure:3666: $? = 0
+configure:3666: result: yes
+configure:3675: checking for inflate in -lz
+configure:3700: gcc34 -o conftest -g -O2   conftest.c -lz   >&5
+configure:3700: $? = 0
+configure:3709: result: yes
+configure:4109: creating ./config.status
+
+## ---------------------- ##
+## Running config.status. ##
+## ---------------------- ##
+
+This file was extended by HTSlib config.status 1.3, which was
+generated by GNU Autoconf 2.69.  Invocation command line was
+
+  CONFIG_FILES    = 
+  CONFIG_HEADERS  = 
+  CONFIG_LINKS    = 
+  CONFIG_COMMANDS = 
+  $ ./config.status 
+
+on hgwdev
+
+config.status:813: creating config.mk
+config.status:813: creating config.h
+config.status:983: config.h is unchanged
+
+## ---------------- ##
+## Cache variables. ##
+## ---------------- ##
+
+ac_cv_c_compiler_gnu=yes
+ac_cv_env_CC_set=set
+ac_cv_env_CC_value=gcc34
+ac_cv_env_CFLAGS_set=
+ac_cv_env_CFLAGS_value=
+ac_cv_env_CPPFLAGS_set=
+ac_cv_env_CPPFLAGS_value=
+ac_cv_env_CPP_set=
+ac_cv_env_CPP_value=
+ac_cv_env_LDFLAGS_set=
+ac_cv_env_LDFLAGS_value=
+ac_cv_env_LIBS_set=
+ac_cv_env_LIBS_value=
+ac_cv_env_build_alias_set=
+ac_cv_env_build_alias_value=
+ac_cv_env_host_alias_set=
+ac_cv_env_host_alias_value=
+ac_cv_env_target_alias_set=
+ac_cv_env_target_alias_value=
+ac_cv_func_getpagesize=yes
+ac_cv_func_gmtime_r=yes
+ac_cv_func_mmap_fixed_mapped=yes
+ac_cv_header_inttypes_h=yes
+ac_cv_header_memory_h=yes
+ac_cv_header_stdc=yes
+ac_cv_header_stdint_h=yes
+ac_cv_header_stdlib_h=yes
+ac_cv_header_string_h=yes
+ac_cv_header_strings_h=yes
+ac_cv_header_sys_param_h=yes
+ac_cv_header_sys_stat_h=yes
+ac_cv_header_sys_types_h=yes
+ac_cv_header_unistd_h=yes
+ac_cv_header_zlib_h=yes
+ac_cv_lib_z_inflate=yes
+ac_cv_objext=o
+ac_cv_path_EGREP='/bin/grep -E'
+ac_cv_path_GREP=/bin/grep
+ac_cv_prog_CPP='gcc34 -E'
+ac_cv_prog_ac_ct_CC=gcc34
+ac_cv_prog_ac_ct_RANLIB=ranlib
+ac_cv_prog_cc_c89=
+ac_cv_prog_cc_g=yes
+
+## ----------------- ##
+## Output variables. ##
+## ----------------- ##
+
+CC='gcc34'
+CFLAGS='-g -O2'
+CPP='gcc34 -E'
+CPPFLAGS=''
+CRYPTO_LIBS=''
+DEFS='-DHAVE_CONFIG_H'
+ECHO_C=''
+ECHO_N='-n'
+ECHO_T=''
+EGREP='/bin/grep -E'
+EXEEXT=''
+GREP='/bin/grep'
+LDFLAGS=''
+LIBOBJS=''
+LIBS=''
+LTLIBOBJS=''
+OBJEXT='o'
+PACKAGE_BUGREPORT='samtools-help@lists.sourceforge.net'
+PACKAGE_NAME='HTSlib'
+PACKAGE_STRING='HTSlib 1.3'
+PACKAGE_TARNAME='htslib'
+PACKAGE_URL='http://www.htslib.org/'
+PACKAGE_VERSION='1.3'
+PATH_SEPARATOR=':'
+RANLIB='ranlib'
+SHELL='/bin/sh'
+ac_ct_CC='gcc34'
+bindir='${exec_prefix}/bin'
+build_alias=''
+datadir='${datarootdir}'
+datarootdir='${prefix}/share'
+define_IRODS_HOME='IRODS_HOME ?= /disabled'
+docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
+dvidir='${docdir}'
+enable_plugins='no'
+exec_prefix='${prefix}'
+host_alias=''
+htmldir='${docdir}'
+includedir='${prefix}/include'
+infodir='${datarootdir}/info'
+irods='disabled'
+libcurl='disabled'
+libdir='${exec_prefix}/lib'
+libexecdir='${exec_prefix}/libexec'
+localedir='${datarootdir}/locale'
+localstatedir='${prefix}/var'
+mandir='${datarootdir}/man'
+oldincludedir='/usr/include'
+pdfdir='${docdir}'
+plugindir='$(libexecdir)/htslib'
+pluginpath='$(libexecdir)/htslib'
+prefix='/usr/local'
+program_transform_name='s,x,x,'
+psdir='${docdir}'
+sbindir='${exec_prefix}/sbin'
+sharedstatedir='${prefix}/com'
+sysconfdir='${prefix}/etc'
+target_alias=''
+
+## ----------- ##
+## confdefs.h. ##
+## ----------- ##
+
+/* confdefs.h */
+#define PACKAGE_NAME "HTSlib"
+#define PACKAGE_TARNAME "htslib"
+#define PACKAGE_VERSION "1.3"
+#define PACKAGE_STRING "HTSlib 1.3"
+#define PACKAGE_BUGREPORT "samtools-help@lists.sourceforge.net"
+#define PACKAGE_URL "http://www.htslib.org/"
+#define STDC_HEADERS 1
+#define HAVE_SYS_TYPES_H 1
+#define HAVE_SYS_STAT_H 1
+#define HAVE_STDLIB_H 1
+#define HAVE_STRING_H 1
+#define HAVE_MEMORY_H 1
+#define HAVE_STRINGS_H 1
+#define HAVE_INTTYPES_H 1
+#define HAVE_STDINT_H 1
+#define HAVE_UNISTD_H 1
+#define HAVE_STDLIB_H 1
+#define HAVE_UNISTD_H 1
+#define HAVE_SYS_PARAM_H 1
+#define HAVE_GETPAGESIZE 1
+#define HAVE_MMAP 1
+#define HAVE_GMTIME_R 1
+#define HAVE_LIBZ 1
+
+configure: exit 0