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414 lines
18 KiB
414 lines
18 KiB
--- a/config.mk.in
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+++ b/config.mk.in
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@@ -28,27 +28,26 @@
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# in the Makefile to reflect your configuration choices. If you don't run
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# configure, the main Makefile contains suitable conservative defaults.
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-prefix = @prefix@
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-exec_prefix = @exec_prefix@
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-bindir = @bindir@
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-datarootdir = @datarootdir@
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-mandir = @mandir@
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+prefix = @prefix@
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+exec_prefix = @exec_prefix@
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+bindir = @bindir@
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+libdir = @libdir@
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+datarootdir = @datarootdir@
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+mandir = @mandir@
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+man1dir = $(mandir)/man1
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CC = @CC@
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+AR = @AR@
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CPPFLAGS = @CPPFLAGS@
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CFLAGS = @CFLAGS@
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LDFLAGS = @LDFLAGS@
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LIBS = @LIBS@
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-@Hsource@HTSDIR = @HTSDIR@
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-@Hsource@include $(HTSDIR)/htslib.mk
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-@Hsource@include $(HTSDIR)/htslib_static.mk
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-@Hsource@HTSLIB = $(HTSDIR)/libhts.a
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-@Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS)
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-@Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
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-@Hsource@BGZIP = $(HTSDIR)/bgzip
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-HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@
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-@Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@
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-@Hinstall@HTSLIB_LIB = -lhts
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+HTSLIB_CFLAGS = @HTSLIB_CFLAGS@
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+HTSLIB_LIBS = @HTSLIB_LIBS@
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-CURSES_LIB = @CURSES_LIB@
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+NCURSES_CFLAGS = @NCURSES_CFLAGS@
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+NCURSES_LIBS = @NCURSES_LIBS@
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+
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+ZLIB_CFLAGS = @ZLIB_CFLAGS@
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+ZLIB_LIBS = @ZLIB_LIBS@
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--- a/configure.ac
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+++ b/configure.ac
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@@ -29,9 +29,6 @@
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AC_CONFIG_SRCDIR([bamtk.c])
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AC_CONFIG_HEADERS([config.h])
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-m4_include([m4/ax_with_curses.m4])
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-m4_include([m4/ax_with_htslib.m4])
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-
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dnl Copyright notice to be copied into the generated configure script
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AC_COPYRIGHT([Portions copyright (C) 2015 Genome Research Ltd.
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@@ -39,73 +36,27 @@
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redistribute it. There is NO WARRANTY, to the extent permitted by law.])
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AC_PROG_CC
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+AM_PROG_AR
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AC_SYS_LARGEFILE
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-AX_WITH_HTSLIB
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-if test "$ax_cv_htslib" != yes; then
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- AC_MSG_ERROR([HTSlib development files not found
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-
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-Samtools uses HTSlib to parse bioinformatics file formats etc. Building it
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-requires an unpacked HTSlib source tree (which will be built in conjunction
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-with samtools) or a previously-installed HTSlib. In either case you may
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-need to configure --with-htslib=DIR to locate the appropriate HTSlib.
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-
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-FAILED. You must supply an HTSlib in order to build samtools successfully.])
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-fi
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-
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-if test "$ax_cv_htslib_which" = source; then
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- Hsource=
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- Hinstall='#'
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-else
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- Hsource='#'
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- Hinstall=
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-fi
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-AC_SUBST([Hsource])
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-AC_SUBST([Hinstall])
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+dnl htslib
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+PKG_CHECK_MODULES([HTSLIB], [htslib])
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+dnl ncurses
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AC_ARG_WITH([curses],
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[AS_HELP_STRING([--without-curses],
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[omit curses support, so no curses library needed])])
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-if test "$with_curses" != no; then
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- AX_WITH_CURSES
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- if test "$ax_cv_curses" != yes; then
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- AC_MSG_ERROR([curses development files not found
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-
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-The 'samtools tview' command uses the curses text user interface library.
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-Building samtools with tview requires curses/ncurses/etc development files
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-to be installed on the build machine; you may need to ensure a package such
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-as libncurses5-dev (on Debian or Ubuntu Linux) or ncurses-devel (on RPM-based
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-Linux distributions) is installed.
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-
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-FAILED. Either configure --without-curses or resolve this error to build
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-samtools successfully.])
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- fi
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-else
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- CURSES_LIB=
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- CURSES_CPPFLAGS=
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- AC_SUBST([CURSES_LIB])
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- AC_SUBST([CURSES_CPPFLAGS])
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-fi
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-
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-save_LIBS=$LIBS
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-zlib_devel=ok
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-dnl Set a trivial non-empty INCLUDES to avoid excess default includes tests
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-AC_CHECK_HEADER([zlib.h], [], [zlib_devel=missing], [;])
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-AC_CHECK_LIB(z, inflate, [], [zlib_devel=missing])
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-LIBS=$save_LIBS
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-
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-if test $zlib_devel != ok; then
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- AC_MSG_ERROR([zlib development files not found
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-
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-Samtools uses compression routines from the zlib library <http://zlib.net>.
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-Building samtools requires zlib development files to be installed on the build
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-machine; you may need to ensure a package such as zlib1g-dev (on Debian or
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-Ubuntu Linux) or zlib-devel (on RPM-based Linux distributions) is installed.
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+AS_IF([test "x$with_curses" != "xno"], [
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+ PKG_CHECK_MODULES([NCURSES], [ncurses])
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+
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+ AC_DEFINE([HAVE_CURSES], [1])
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+ AC_DEFINE([HAVE_NCURSES_H], [1])
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+])
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-FAILED. This error must be resolved in order to build samtools successfully.])
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-fi
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+dnl zlib
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+PKG_CHECK_MODULES([ZLIB], [zlib])
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AC_CONFIG_FILES([config.mk])
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AC_OUTPUT
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--- a/Makefile
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+++ b/Makefile
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@@ -21,14 +21,6 @@
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# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
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# DEALINGS IN THE SOFTWARE.
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-CC = gcc
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-AR = ar
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-CPPFLAGS =
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-#CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
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-CFLAGS = -g -Wall -O2
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-LDFLAGS =
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-LIBS =
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-
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LOBJS= bam_aux.o bam.o bam_import.o sam.o \
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sam_header.o bam_plbuf.o
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AOBJS= bam_index.o bam_plcmd.o sam_view.o \
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@@ -40,13 +32,6 @@
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bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
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bam_quickcheck.o bam_addrprg.o
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-prefix = /usr/local
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-exec_prefix = $(prefix)
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-bindir = $(exec_prefix)/bin
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-datarootdir = $(prefix)/share
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-mandir = $(datarootdir)/man
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-man1dir = $(mandir)/man1
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-
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# Installation location for $(MISC_PROGRAMS) and $(MISC_SCRIPTS)
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misc_bindir = $(bindir)
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@@ -85,15 +70,14 @@
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all: $(PROGRAMS) $(MISC_PROGRAMS) $(TEST_PROGRAMS)
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-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
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-ALL_LDFLAGS = $(HTSLIB_LDFLAGS) $(LDFLAGS)
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-ALL_LIBS = -lz $(LIBS)
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+ALL_CPPFLAGS = -I. $(HTSLIB_CFLAGS) $(CPPFLAGS)
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+ALL_LIBS = $(ZLIB_LIBS) $(LIBS)
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# Usually config.mk and config.h are generated by running configure
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# or config.status, but if those aren't used create defaults here.
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config.mk:
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- @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CPPFLAGS@/-I$$(HTSDIR)/g;s/@CURSES_LIB@/-lcurses/g' config.mk.in > $@
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+ @sed -e '/^prefix/,/^LIBS/d;s/@Hsource@//;s/@Hinstall@/#/;s#@HTSDIR@#htslib-1.5#g;s/@HTSLIB_CFLAGS@/-I$$(HTSDIR)/g;s/@NCURSES_LIBS@/-lcurses/g' config.mk.in > $@
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config.h:
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echo '/* Basic config.h generated by Makefile */' > $@
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@@ -133,17 +117,22 @@
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.c.o:
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$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
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+$(LOBJS):
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+ $(CC) $(CFLAGS) $(ALL_CPPFLAGS) -fPIC -c -o $@ $<
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+
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LIBST_OBJS = sam_opts.o sam_utils.o
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-lib:libbam.a
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+lib: libbam.so.1.0
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-libbam.a:$(LOBJS)
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- $(AR) -csru $@ $(LOBJS)
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+libbam.so.1.0:$(LOBJS)
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+ $(CC) $(CFLAGS) $(LDFLAGS) -shared -Wl,--soname,$@ -o $@ $(LOBJS) $(HTSLIB)
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+ ln -sf $@ libbam.so.1
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+ ln -sf $@ libbam.so
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-samtools: $(AOBJS) libbam.a libst.a $(HTSLIB)
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- $(CC) $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a libst.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) -lpthread
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+samtools: $(AOBJS) libbam.so.1.0 libst.a
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ $(AOBJS) libbam.so.1.0 libst.a $(HTSLIB_LIBS) $(NCURSES_LIBS) -lm $(ALL_LIBS) -lpthread
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# For building samtools and its test suite only: NOT to be installed.
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libst.a: $(LIBST_OBJS)
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@@ -151,58 +140,58 @@
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$(AR) -rcs $@ $(LIBST_OBJS)
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-bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
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-bam2bcf_h = bam2bcf.h $(htslib_hts_h) $(htslib_vcf_h)
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-bam_lpileup_h = bam_lpileup.h $(htslib_sam_h)
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-bam_plbuf_h = bam_plbuf.h $(htslib_sam_h)
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-bam_tview_h = bam_tview.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) $(bam2bcf_h) $(htslib_khash_h) $(bam_lpileup_h)
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-sam_h = sam.h $(htslib_sam_h) $(bam_h)
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-sam_opts_h = sam_opts.h $(htslib_hts_h)
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-sample_h = sample.h $(htslib_kstring_h)
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-
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-bam.o: bam.c config.h $(bam_h) $(htslib_kstring_h) sam_header.h
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-bam2bcf.o: bam2bcf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(htslib_kfunc_h) $(bam2bcf_h)
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-bam2bcf_indel.o: bam2bcf_indel.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam2bcf_h) $(htslib_khash_h) $(htslib_ksort_h)
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-bam2depth.o: bam2depth.c config.h $(htslib_sam_h) samtools.h $(sam_opts_h)
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-bam_addrprg.o: bam_addrprg.c config.h $(htslib_sam_h) $(htslib_kstring_h) samtools.h $(sam_opts_h)
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+bam_h = bam.h
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+bam2bcf_h = bam2bcf.h
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+bam_lpileup_h = bam_lpileup.h
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+bam_plbuf_h = bam_plbuf.h
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+bam_tview_h = bam_tview.h $(bam2bcf_h) $(bam_lpileup_h)
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+sam_h = sam.h $(bam_h)
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+sam_opts_h = sam_opts.h
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+sample_h = sample.h
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+
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+bam.o: bam.c config.h $(bam_h) sam_header.h
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+bam2bcf.o: bam2bcf.c config.h $(bam2bcf_h)
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+bam2bcf_indel.o: bam2bcf_indel.c config.h $(bam2bcf_h)
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+bam2depth.o: bam2depth.c config.h samtools.h $(sam_opts_h)
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+bam_addrprg.o: bam_addrprg.c config.h samtools.h $(sam_opts_h)
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bam_aux.o: bam_aux.c config.h $(bam_h)
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-bam_cat.o: bam_cat.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_cram_h) $(htslib_khash_h) samtools.h
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+bam_cat.o: bam_cat.c config.h samtools.h
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bam_color.o: bam_color.c config.h $(bam_h)
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-bam_import.o: bam_import.c config.h $(htslib_kstring_h) $(bam_h) $(htslib_kseq_h)
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-bam_index.o: bam_index.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_khash_h) samtools.h
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-bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h) $(htslib_ksort_h)
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-bam_mate.o: bam_mate.c config.h $(sam_opts_h) $(htslib_kstring_h) $(htslib_sam_h) samtools.h
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-bam_md.o: bam_md.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h
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-bam_plbuf.o: bam_plbuf.c config.h $(htslib_hts_h) $(htslib_sam_h) $(bam_plbuf_h)
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-bam_plcmd.o: bam_plcmd.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_str2int_h) sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h)
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-bam_quickcheck.o: bam_quickcheck.c config.h $(htslib_hts_h) $(htslib_sam_h)
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-bam_reheader.o: bam_reheader.c config.h $(htslib_bgzf_h) $(htslib_sam_h) $(htslib_hfile_h) $(htslib_cram_h) samtools.h
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-bam_rmdup.o: bam_rmdup.c config.h $(htslib_sam_h) $(sam_opts_h) samtools.h $(bam_h) $(htslib_khash_h)
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-bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) $(htslib_sam_h) $(htslib_khash_h) $(htslib_klist_h) samtools.h
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-bam_sort.o: bam_sort.c config.h $(htslib_ksort_h) $(htslib_khash_h) $(htslib_klist_h) $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) samtools.h
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-bam_split.o: bam_split.c config.h $(htslib_sam_h) $(htslib_khash_h) $(htslib_kstring_h) $(htslib_cram_h) $(sam_opts_h) samtools.h
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-bam_stat.o: bam_stat.c config.h $(htslib_sam_h) samtools.h
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-bam_tview.o: bam_tview.c config.h $(bam_tview_h) $(htslib_faidx_h) $(htslib_sam_h) $(htslib_bgzf_h) samtools.h $(sam_opts_h)
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+bam_import.o: bam_import.c config.h $(bam_h)
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+bam_index.o: bam_index.c config.h samtools.h
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+bam_lpileup.o: bam_lpileup.c config.h $(bam_plbuf_h) $(bam_lpileup_h)
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+bam_mate.o: bam_mate.c config.h $(sam_opts_h) samtools.h
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+bam_md.o: bam_md.c config.h $(sam_opts_h) samtools.h
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+bam_plbuf.o: bam_plbuf.c config.h $(bam_plbuf_h)
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+bam_plcmd.o: bam_plcmd.c config.h sam_header.h samtools.h $(sam_opts_h) $(bam2bcf_h) $(sample_h)
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+bam_quickcheck.o: bam_quickcheck.c config.h
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+bam_reheader.o: bam_reheader.c config.h samtools.h
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+bam_rmdup.o: bam_rmdup.c config.h $(sam_opts_h) samtools.h $(bam_h)
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+bam_rmdupse.o: bam_rmdupse.c config.h $(bam_h) samtools.h
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+bam_sort.o: bam_sort.c config.h $(sam_opts_h) samtools.h
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+bam_split.o: bam_split.c config.h $(sam_opts_h) samtools.h
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+bam_stat.o: bam_stat.c config.h samtools.h
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+bam_tview.o: bam_tview.c config.h $(bam_tview_h) samtools.h $(sam_opts_h)
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bam_tview_curses.o: bam_tview_curses.c config.h $(bam_tview_h)
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bam_tview_html.o: bam_tview_html.c config.h $(bam_tview_h)
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-bam_flags.o: bam_flags.c config.h $(htslib_sam_h)
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-bamshuf.o: bamshuf.c config.h $(htslib_sam_h) $(htslib_hts_h) $(htslib_ksort_h) samtools.h $(sam_opts_h)
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-bamtk.o: bamtk.c config.h $(htslib_hts_h) samtools.h version.h
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-bedcov.o: bedcov.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(sam_opts_h) $(htslib_kseq_h)
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-bedidx.o: bedidx.c config.h $(htslib_ksort_h) $(htslib_kseq_h) $(htslib_khash_h)
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-cut_target.o: cut_target.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_faidx_h) samtools.h $(sam_opts_h)
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-dict.o: dict.c config.h $(htslib_kseq_h) $(htslib_hts_h)
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-faidx.o: faidx.c config.h $(htslib_faidx_h) samtools.h
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-padding.o: padding.c config.h $(htslib_kstring_h) $(htslib_sam_h) $(htslib_faidx_h) sam_header.h $(sam_opts_h) samtools.h
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-phase.o: phase.c config.h $(htslib_hts_h) $(htslib_sam_h) $(htslib_kstring_h) $(sam_opts_h) samtools.h $(htslib_kseq_h) $(htslib_khash_h) $(htslib_ksort_h)
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-sam.o: sam.c config.h $(htslib_faidx_h) $(sam_h)
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-sam_header.o: sam_header.c config.h sam_header.h $(htslib_khash_h)
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+bam_flags.o: bam_flags.c config.h
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+bamshuf.o: bamshuf.c config.h samtools.h $(sam_opts_h)
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+bamtk.o: bamtk.c config.h samtools.h version.h
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+bedcov.o: bedcov.c config.h $(sam_opts_h)
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+bedidx.o: bedidx.c config.h
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+cut_target.o: cut_target.c config.h samtools.h $(sam_opts_h)
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+dict.o: dict.c config.h
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+faidx.o: faidx.c config.h samtools.h
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+padding.o: padding.c config.h sam_header.h $(sam_opts_h) samtools.h
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+phase.o: phase.c config.h $(sam_opts_h) samtools.h
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+sam.o: sam.c config.h $(sam_h)
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+sam_header.o: sam_header.c config.h sam_header.h
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sam_opts.o: sam_opts.c config.h $(sam_opts_h)
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sam_utils.o: sam_utils.c config.h samtools.h
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-sam_view.o: sam_view.c config.h $(htslib_sam_h) $(htslib_faidx_h) $(htslib_kstring_h) $(htslib_khash_h) samtools.h $(sam_opts_h)
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-sample.o: sample.c config.h $(sample_h) $(htslib_khash_h)
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-stats_isize.o: stats_isize.c config.h stats_isize.h $(htslib_khash_h)
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-stats.o: stats.c config.h $(htslib_faidx_h) $(htslib_sam_h) $(htslib_hts_h) sam_header.h $(htslib_khash_str2int_h) samtools.h $(htslib_khash_h) $(htslib_kstring_h) stats_isize.h $(sam_opts_h)
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+sam_view.o: sam_view.c config.h samtools.h $(sam_opts_h)
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+sample.o: sample.c config.h $(sample_h)
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+stats_isize.o: stats_isize.c config.h stats_isize.h
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+stats.o: stats.c config.h sam_header.h samtools.h stats_isize.h $(sam_opts_h)
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# test programs
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@@ -224,30 +213,30 @@
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test/merge/test_bam_translate: test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB)
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- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_bam_translate.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
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test/merge/test_rtrans_build: test/merge/test_rtrans_build.o libst.a $(HTSLIB)
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- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_rtrans_build.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
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test/merge/test_trans_tbl_init: test/merge/test_trans_tbl_init.o libst.a $(HTSLIB)
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- $(CC) $(ALL_LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/merge/test_trans_tbl_init.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
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test/split/test_count_rg: test/split/test_count_rg.o test/test.o libst.a $(HTSLIB)
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- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_count_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
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test/split/test_expand_format_string: test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB)
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- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_expand_format_string.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
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test/split/test_filter_header_rg: test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB)
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|
- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
|
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+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_filter_header_rg.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
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|
test/split/test_parse_args: test/split/test_parse_args.o test/test.o libst.a $(HTSLIB)
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|
- $(CC) $(ALL_LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
|
|
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/split/test_parse_args.o test/test.o libst.a $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
|
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|
|
test/vcf-miniview: test/vcf-miniview.o $(HTSLIB)
|
|
- $(CC) $(ALL_LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIB) $(ALL_LIBS) -lpthread
|
|
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ test/vcf-miniview.o $(HTSLIB_LIBS) $(ALL_LIBS) -lpthread
|
|
|
|
-test_test_h = test/test.h $(htslib_sam_h)
|
|
+test_test_h = test/test.h
|
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|
|
test/merge/test_bam_translate.o: test/merge/test_bam_translate.c config.h bam_sort.o $(test_test_h)
|
|
test/merge/test_rtrans_build.o: test/merge/test_rtrans_build.c config.h bam_sort.o
|
|
@@ -256,34 +245,34 @@
|
|
test/split/test_expand_format_string.o: test/split/test_expand_format_string.c config.h bam_split.o $(test_test_h)
|
|
test/split/test_filter_header_rg.o: test/split/test_filter_header_rg.c config.h bam_split.o $(test_test_h)
|
|
test/split/test_parse_args.o: test/split/test_parse_args.c config.h bam_split.o $(test_test_h)
|
|
-test/test.o: test/test.c config.h $(htslib_sam_h) $(test_test_h)
|
|
-test/vcf-miniview.o: test/vcf-miniview.c config.h $(htslib_vcf_h)
|
|
+test/test.o: test/test.c config.h $(test_test_h)
|
|
+test/vcf-miniview.o: test/vcf-miniview.c config.h
|
|
|
|
|
|
# misc programs
|
|
|
|
misc/ace2sam: misc/ace2sam.o
|
|
- $(CC) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS)
|
|
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/ace2sam.o $(ALL_LIBS)
|
|
|
|
misc/maq2sam-short: misc/maq2sam-short.o
|
|
- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS)
|
|
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-short.o $(ALL_LIBS)
|
|
|
|
misc/maq2sam-long: misc/maq2sam-long.o
|
|
- $(CC) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS)
|
|
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/maq2sam-long.o $(ALL_LIBS)
|
|
|
|
misc/md5fa: misc/md5fa.o $(HTSLIB)
|
|
- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIB) $(ALL_LIBS)
|
|
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5fa.o $(HTSLIB_LIBS) $(ALL_LIBS)
|
|
|
|
misc/md5sum-lite: misc/md5sum-lite.o $(HTSLIB)
|
|
- $(CC) $(ALL_LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIB) $(ALL_LIBS)
|
|
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/md5sum-lite.o $(HTSLIB_LIBS) $(ALL_LIBS)
|
|
|
|
misc/wgsim: misc/wgsim.o
|
|
- $(CC) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS)
|
|
+ $(CC) $(CFLAGS) $(LDFLAGS) -o $@ misc/wgsim.o -lm $(ALL_LIBS)
|
|
|
|
-misc/ace2sam.o: misc/ace2sam.c config.h $(htslib_kstring_h) $(htslib_kseq_h)
|
|
-misc/md5fa.o: misc/md5fa.c config.h $(htslib_kseq_h) $(htslib_hts_h)
|
|
-misc/md5sum-lite.o: misc/md5sum-lite.c config.h $(htslib_hts_h)
|
|
-misc/wgsim.o: misc/wgsim.c config.h $(htslib_kseq_h)
|
|
+misc/ace2sam.o: misc/ace2sam.c config.h
|
|
+misc/md5fa.o: misc/md5fa.c config.h
|
|
+misc/md5sum-lite.o: misc/md5sum-lite.c config.h
|
|
+misc/wgsim.o: misc/wgsim.c config.h
|
|
|
|
misc/maq2sam-short.o: misc/maq2sam.c config.h
|
|
$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ misc/maq2sam.c
|