dc1d64b572
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction with bcftools), and a simple alignment viewer. WWW: http://www.htslib.org/ PR: 195592 Submitted by: Reed A. Cartwright <cartwright@asu.edu>
85 lines
2.6 KiB
Text
85 lines
2.6 KiB
Text
--- Makefile.orig 2014-09-19 15:51:42 UTC
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+++ Makefile
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@@ -21,12 +21,12 @@
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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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-CPPFLAGS = $(DFLAGS) $(INCLUDES)
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-CFLAGS = -g -Wall -O2
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-LDFLAGS =
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-LDLIBS =
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-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1
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+CC ?= cc
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+CPPFLAGS += $(DFLAGS) $(INCLUDES)
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+CFLAGS += -Wall -Wno-unused-function -Wno-implicit-function-declaration
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+LDFLAGS +=
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+LDLIBS +=
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+DFLAGS= -D_CURSES_LIB=1
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LOBJS= bam_aux.o bam.o bam_import.o sam.o \
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sam_header.o bam_plbuf.o
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AOBJS= bam_index.o bam_plcmd.o sam_view.o \
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@@ -39,19 +39,12 @@ AOBJS= bam_index.o bam_plcmd.o sam_
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INCLUDES= -I. -I$(HTSDIR)
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LIBCURSES= -lcurses # -lXCurses
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-prefix = /usr/local
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+prefix = ${STAGEDIR}${PREFIX}
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exec_prefix = $(prefix)
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bindir = $(exec_prefix)/bin
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-mandir = $(prefix)/share/man
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+mandir = $(prefix)/man
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man1dir = $(mandir)/man1
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-MKDIR_P = mkdir -p
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-INSTALL = install -p
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-INSTALL_PROGRAM = $(INSTALL)
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-INSTALL_DATA = $(INSTALL) -m 644
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-INSTALL_DIR = $(MKDIR_P) -m 755
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-
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-
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PROGRAMS = samtools
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BUILT_MISC_PROGRAMS = \
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@@ -59,7 +52,6 @@ BUILT_MISC_PROGRAMS = \
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misc/md5fa misc/md5sum-lite misc/wgsim
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MISC_PROGRAMS = \
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- $(BUILT_MISC_PROGRAMS) \
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misc/blast2sam.pl misc/bowtie2sam.pl misc/export2sam.pl \
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misc/interpolate_sam.pl misc/novo2sam.pl \
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misc/plot-bamstats misc/psl2sam.pl \
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@@ -82,9 +74,8 @@ all: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
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# Adjust $(HTSDIR) to point to your top-level htslib directory
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-HTSDIR = ../htslib
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-include $(HTSDIR)/htslib.mk
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-HTSLIB = $(HTSDIR)/libhts.a
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+HTSDIR = $(prefix)/include
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+HTSLIB = -lhts
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BGZIP = $(HTSDIR)/bgzip
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@@ -121,7 +112,7 @@ lib:libbam.a
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libbam.a:$(LOBJS)
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$(AR) -csru $@ $(LOBJS)
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-samtools: $(AOBJS) libbam.a $(HTSLIB)
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+samtools: $(AOBJS) libbam.a
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$(CC) -pthread $(LDFLAGS) -o $@ $(AOBJS) libbam.a $(HTSLIB) $(LDLIBS) $(LIBCURSES) -lm -lz
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bam_h = bam.h $(htslib_bgzf_h) $(htslib_sam_h)
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@@ -269,8 +260,10 @@ misc/md5sum-lite.o: misc/md5.c misc/md5.
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install: $(PROGRAMS) $(BUILT_MISC_PROGRAMS)
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- $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(man1dir)
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- $(INSTALL_PROGRAM) $(PROGRAMS) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)
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+ $(INSTALL_DIR) $(DESTDIR)$(bindir) $(DESTDIR)$(bindir)/samtools_misc $(DESTDIR)$(man1dir)
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+ $(INSTALL_PROGRAM) $(PROGRAMS) $(DESTDIR)$(bindir)
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+ $(INSTALL_PROGRAM) $(BUILT_MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
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+ $(INSTALL_SCRIPT) $(MISC_PROGRAMS) $(DESTDIR)$(bindir)/samtools_misc
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$(INSTALL_DATA) samtools.1 $(DESTDIR)$(man1dir)
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