# Optional configure Makefile overrides for bcftools.

#

# Copyright (C) 2015,2017, 2019 Genome Research Ltd.

#

# Author: John Marshall <[email protected]>

#

# 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@

libexecdir = @libexecdir@

datarootdir = @datarootdir@

mandir = @mandir@

CC = @CC@

CPPFLAGS = @CPPFLAGS@

CFLAGS = @CFLAGS@

LDFLAGS = @LDFLAGS@

LIBS = @LIBS@

DYNAMIC_FLAGS = @CC_RDYNAMIC_OPT@

USE_GPL = @USE_GPL@

GSL_LIBS = @GSL_LIBS@

PERL_CFLAGS = @PERL_CCOPTS@

PERL_LIBS = @PERL_LIBS@

PLATFORM = @PLATFORM@

PLUGINS_ENABLED = @enable_bcftools_plugins@

plugindir = @bcf_plugindir@

pluginpath = @bcf_pluginpath@

PLUGIN_EXT = @PLUGIN_EXT@

@Hsource@HTSDIR = @HTSDIR@

@Hsource@include $(HTSDIR)/htslib.mk

@Hsource@include $(HTSDIR)/htslib_static.mk

@Hsource@HTSLIB = $(HTSDIR)/libhts.a

@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS)

@Hsource@HTSLIB_DLL = $(HTSDIR)/@HTSLIB_DLL@

@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)

@Hsource@W32_PLUGIN_LIBS = libbcftools.a $(HTSLIB_DLL) $(ALL_LIBS)

@Hsource@BGZIP = $(HTSDIR)/bgzip

@Hsource@TABIX = $(HTSDIR)/tabix

HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@

@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@

@Hinstall@HTSLIB_LIB = -lhts

@Hinstall@W32_PLUGIN_LIBS = libbcftools.a $(HTSLIB_LDFLAGS) $(HTSLIB_LIB) $(ALL_LIBS)