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/configure.ac src/htslib/configure.ac
new file mode 100644
index 0000000..27fa1f4
--- /dev/null
+++ src/htslib/configure.ac
@@ -0,0 +1,192 @@
+# Configure script for htslib, a C library for high-throughput sequencing data.
+#
+#    Copyright (C) 2015 Genome Research Ltd.
+#
+#    Author: John Marshall <jm18@sanger.ac.uk>
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# 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.
+
+dnl Process this file with autoconf to produce a configure script
+AC_INIT([HTSlib], m4_esyscmd_s([make print-version]),
+        [samtools-help@lists.sourceforge.net], [], [http://www.htslib.org/])
+AC_PREREQ(2.63)  dnl This version introduced 4-argument AC_CHECK_HEADER
+AC_CONFIG_SRCDIR(hts.c)
+AC_CONFIG_HEADERS(config.h)
+
+dnl Copyright notice to be copied into the generated configure script
+AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.
+
+This configure script is free software: you are free to change and
+redistribute it.  There is NO WARRANTY, to the extent permitted by law.])
+
+AC_PROG_CC
+AC_PROG_RANLIB
+
+need_crypto=no
+
+AC_ARG_WITH([irods],
+  [AS_HELP_STRING([[--with-irods[=DIR]]],
+                  [use RodsAPIs library (in DIR) to support iRODS URLs])],
+  [case $withval in
+     no)  irods=disabled ;;
+     yes) irods=enabled ;;
+     *)   irods=enabled; IRODS_HOME=$withval ;;
+   esac],
+  [irods=disabled])
+
+AC_ARG_ENABLE([libcurl],
+  [AS_HELP_STRING([--enable-libcurl],
+                  [enable libcurl-based support for http/https/etc URLs])],
+  [], [enable_libcurl=no])
+
+AC_ARG_ENABLE([plugins],
+  [AS_HELP_STRING([--enable-plugins],
+                  [enable separately-compiled plugins for file access])],
+  [], [enable_plugins=no])
+AC_SUBST(enable_plugins)
+
+AC_ARG_WITH([plugin-dir],
+  [AS_HELP_STRING([--with-plugin-dir=DIR],
+                  [plugin installation location [LIBEXECDIR/htslib]])],
+  [case $withval in
+     yes|no) AC_MSG_ERROR([no directory specified for --with-plugin-dir]) ;;
+   esac],
+   [with_plugin_dir='$(libexecdir)/htslib'])
+AC_SUBST([plugindir], $with_plugin_dir)
+
+AC_ARG_WITH([plugin-path],
+  [AS_HELP_STRING([--with-plugin-path=PATH],
+                  [default HTS_PATH plugin search path [PLUGINDIR]])],
+  [case $withval in
+     yes) AC_MSG_ERROR([no path specified for --with-plugin-path]) ;;
+     no)  with_plugin_path= ;;
+   esac],
+  [with_plugin_path=$with_plugin_dir])
+AC_SUBST([pluginpath], $with_plugin_path)
+
+dnl FIXME This pulls in dozens of standard header checks
+AC_FUNC_MMAP
+AC_CHECK_FUNCS(gmtime_r)
+
+if test $enable_plugins != no; then
+  AC_SEARCH_LIBS([dlopen], [dl], [],
+    [AC_MSG_ERROR([dlopen() not found
+
+Plugin support requires dynamic linking facilities from the operating system.
+Either configure with --disable-plugins or resolve this error to build HTSlib.])])
+  # TODO Test whether this is required and/or needs tweaking per-platform
+  LDFLAGS="$LDFLAGS -rdynamic"
+  AC_DEFINE([ENABLE_PLUGINS], 1, [Define if HTSlib should enable plugins.])
+fi
+
+save_LIBS=$LIBS
+zlib_devel=ok
+dnl Set a trivial non-empty INCLUDES to avoid excess default includes tests
+AC_CHECK_HEADER([zlib.h], [], [zlib_devel=missing], [;])
+AC_CHECK_LIB(z, inflate,  [], [zlib_devel=missing])
+LIBS=$save_LIBS
+
+if test $zlib_devel != ok; then
+  AC_MSG_ERROR([zlib development files not found
+
+HTSlib uses compression routines from the zlib library <http://zlib.net>.
+Building HTSlib requires zlib development files to be installed on the build
+machine; you may need to ensure a package such as zlib1g-dev (on Debian or
+Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed.
+
+FAILED.  This error must be resolved in order to build HTSlib successfully.])
+fi
+
+if test $irods = enabled; then
+  # TODO Also test whether we require libgssapi_krb5 and AC_CHECK_LIB it
+  save_LDFLAGS=$LDFLAGS
+  LDFLAGS="$LDFLAGS -L$IRODS_HOME/lib/core/obj"
+  AC_CHECK_LIB([RodsAPIs], [getRodsEnvFileName],
+    [case $with_irods in
+       yes) define_IRODS_HOME='# Uses $(IRODS_HOME) from the environment' ;;
+       *)   define_IRODS_HOME="IRODS_HOME = $with_irods" ;;
+     esac],
+    [AC_MSG_ERROR([iRODS development files not found
+
+Support for iRODS URLs requires the libRodsAPI client library and headers.
+Configure with --with-irods=DIR (or just --with-irods if \$IRODS_HOME has
+been exported with a suitable value), where DIR is the base of an iRODS tree
+such that the library is present as DIR/lib/core/obj/libRodsAPI.* and headers
+are present under DIR/lib/api/include and so on.])],
+    [-lgssapi_krb5 -lpthread])
+  LDFLAGS=$save_LDFLAGS
+  AC_DEFINE([HAVE_IRODS], 1, [Define to 1 if iRODS file access is enabled.])
+else
+  define_IRODS_HOME='IRODS_HOME ?= /disabled'
+fi
+AC_SUBST([irods])
+AC_SUBST([define_IRODS_HOME])
+
+libcurl=disabled
+if test "$enable_libcurl" != no; then
+  AC_CHECK_LIB([curl], [curl_easy_pause],
+    [AC_DEFINE([HAVE_LIBCURL], 1, [Define if libcurl file access is enabled.])
+     libcurl=enabled],
+    [AC_CHECK_LIB([curl], [curl_easy_init],
+       [message="library is too old (7.18+ required)"],
+       [message="library not found"])
+     case "$enable_libcurl" in
+       check) AC_MSG_WARN([libcurl not enabled: $message]) ;;
+       *) AC_MSG_ERROR([libcurl $message
+
+Support for HTTPS and other SSL-based URLs requires routines from the libcurl
+library <http://curl.haxx.se/libcurl/>.  Building HTSlib with libcurl enabled
+requires libcurl development files to be installed on the build machine; you
+may need to ensure a package such as libcurl4-{gnutls,nss,openssl}-dev (on
+Debian or Ubuntu Linux) or libcurl-devel (on RPM-based Linux distributions)
+is installed.
+
+Either configure with --disable-libcurl or resolve this error to build HTSlib.])
+       ;;
+     esac])
+  need_crypto=yes
+fi
+AC_SUBST([libcurl])
+
+CRYPTO_LIBS=
+if test $need_crypto != no; then
+  AC_CHECK_FUNC([CCHmac],
+    [AC_DEFINE([HAVE_COMMONCRYPTO], 1,
+               [Define if you have the Common Crypto library.])],
+    [save_LIBS=$LIBS
+     AC_SEARCH_LIBS([HMAC], [crypto],
+       [AC_DEFINE([HAVE_HMAC], 1, [Define if you have libcrypto-style HMAC().])
+        case "$ac_cv_search_HMAC" in
+          -l*) CRYPTO_LIBS=$ac_cv_search_HMAC ;;
+        esac],
+     [AC_MSG_ERROR([SSL development files not found
+
+Support for AWS S3 URLs requires routines from an SSL library.  Building
+HTSlib with libcurl enabled requires SSL development files to be installed
+on the build machine; you may need to ensure a package such as libgnutls-dev,
+libnss3-dev, or libssl-dev (on Debian or Ubuntu Linux, corresponding to the
+libcurl4-*-dev package installed) or similar on RPM-based Linux distributions.
+
+Either configure with --disable-libcurl or resolve this error to build HTSlib.])])
+     LIBS=$save_LIBS])
+fi
+AC_SUBST([CRYPTO_LIBS])
+
+AC_CONFIG_FILES(config.mk)
+AC_OUTPUT