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.mk.in src/htslib/config.mk.in
new file mode 100644
index 0000000..dc8214b
--- /dev/null
+++ src/htslib/config.mk.in
@@ -0,0 +1,111 @@
+#  Optional configure Makefile overrides for htslib.
+#
+#    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.
+
+# This is @configure_input@
+#
+# If you use configure, this file overrides variables and augments rules
+# in the Makefile to reflect your configuration choices.  If you don't run
+# configure, the main Makefile contains suitable conservative defaults.
+
+prefix       = @prefix@
+exec_prefix  = @exec_prefix@
+bindir       = @bindir@
+includedir   = @includedir@
+libdir       = @libdir@
+libexecdir   = @libexecdir@
+datarootdir  = @datarootdir@
+mandir       = @mandir@
+
+CC     = @CC@
+RANLIB = @RANLIB@
+
+CPPFLAGS = @CPPFLAGS@
+CFLAGS   = @CFLAGS@
+LDFLAGS  = @LDFLAGS@
+LIBS     = @LIBS@
+
+# Lowercase here indicates these are "local" to config.mk
+plugin_OBJS =
+noplugin_LDFLAGS =
+noplugin_LIBS =
+
+# ifeq/.../endif, +=, and target-specific variables are GNU Make-specific.
+# If you don't have GNU Make, comment out this conditional and note that
+# to enable iRODS you will need to implement the following elsewhere.
+ifeq "iRODS-@irods@" "iRODS-enabled"
+
+@define_IRODS_HOME@
+
+IRODS_CPPFLAGS = \
+	-I$(IRODS_HOME)/lib/api/include \
+	-I$(IRODS_HOME)/lib/core/include \
+	-I$(IRODS_HOME)/lib/md5/include \
+	-I$(IRODS_HOME)/lib/sha1/include \
+	-I$(IRODS_HOME)/server/core/include \
+	-I$(IRODS_HOME)/server/drivers/include \
+	-I$(IRODS_HOME)/server/icat/include
+
+IRODS_LDFLAGS = -L$(IRODS_HOME)/lib/core/obj
+IRODS_LIBS = -lRodsAPIs -lgssapi_krb5
+
+plugin_OBJS += hfile_irods.o
+
+hfile_irods.o hfile_irods.pico: CPPFLAGS += $(IRODS_CPPFLAGS)
+hfile_irods.so hfile_irods.bundle: LDFLAGS += $(IRODS_LDFLAGS)
+hfile_irods.so hfile_irods.bundle: LIBS += $(IRODS_LIBS)
+
+noplugin_LDFLAGS += $(IRODS_LDFLAGS)
+noplugin_LIBS += $(IRODS_LIBS)
+
+endif
+
+ifeq "libcurl-@libcurl@" "libcurl-enabled"
+
+LIBCURL_LIBS = -lcurl @CRYPTO_LIBS@
+
+plugin_OBJS += hfile_libcurl.o
+
+hfile_libcurl.so hfile_libcurl.bundle: LIBS += $(LIBCURL_LIBS)
+
+noplugin_LIBS += $(LIBCURL_LIBS)
+
+endif
+
+ifeq "plugins-@enable_plugins@" "plugins-yes"
+
+plugindir  = @plugindir@
+pluginpath = @pluginpath@
+
+LIBHTS_OBJS += plugin.o
+PLUGIN_OBJS += $(plugin_OBJS)
+
+plugin.o plugin.pico: CPPFLAGS += -DPLUGINPATH=\"$(pluginpath)\"
+
+else
+
+LIBHTS_OBJS += $(plugin_OBJS)
+LDFLAGS += $(noplugin_LDFLAGS)
+LIBS += $(noplugin_LIBS)
+
+endif