diff PsiCLASS-1.0.2/samtools-0.1.19/Makefile @ 0:903fc43d6227 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/Makefile	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,101 @@
+CC=			gcc
+CFLAGS=		-g -Wall -O2
+#LDFLAGS=		-Wl,-rpath,\$$ORIGIN/../lib
+DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=0
+KNETFILE_O=	knetfile.o
+LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o	\
+			bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o \
+			$(KNETFILE_O) bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
+AOBJS=		bam_tview.o bam_plcmd.o sam_view.o \
+			bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o \
+			bamtk.o kaln.o bam2bcf.o bam2bcf_indel.o errmod.o sample.o \
+			cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \
+			bam_tview_curses.o bam_tview_html.o
+PROG=		samtools
+INCLUDES=	-I.
+SUBDIRS=	. bcftools misc
+LIBPATH=
+LIBCURSES=	 # -lXCurses
+
+.SUFFIXES:.c .o
+.PHONY: all lib
+
+.c.o:
+		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+		@target=`echo $@ | sed s/-recur//`; \
+		wdir=`pwd`; \
+		list='$(SUBDIRS)'; for subdir in $$list; do \
+			cd $$subdir; \
+			$(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CFLAGS="$(CFLAGS)" \
+				INCLUDES="$(INCLUDES)" LIBPATH="$(LIBPATH)" $$target || exit 1; \
+			cd $$wdir; \
+		done;
+
+all:$(PROG)
+
+.PHONY:all lib clean cleanlocal
+.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
+
+lib:libbam.a
+
+libbam.a:$(LOBJS)
+		$(AR) -csru $@ $(LOBJS)
+
+samtools:lib-recur $(AOBJS)
+		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
+
+razip:razip.o razf.o $(KNETFILE_O)
+		$(CC) $(CFLAGS) -o $@ $^ -lz
+
+bgzip:bgzip.o bgzf.o $(KNETFILE_O)
+		$(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
+
+bgzf.o:bgzf.c bgzf.h
+		$(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
+
+razip.o:razf.h
+bam.o:bam.h razf.h bam_endian.h kstring.h sam_header.h
+sam.o:sam.h bam.h
+bam_import.o:bam.h kseq.h khash.h razf.h
+bam_pileup.o:bam.h razf.h ksort.h
+bam_plcmd.o:bam.h faidx.h bcftools/bcf.h bam2bcf.h
+bam_index.o:bam.h khash.h ksort.h razf.h bam_endian.h
+bam_lpileup.o:bam.h ksort.h
+bam_tview.o:bam.h faidx.h bam_tview.h
+bam_tview_curses.o:bam.h faidx.h bam_tview.h
+bam_tview_html.o:bam.h faidx.h bam_tview.h
+bam_sort.o:bam.h ksort.h razf.h
+bam_md.o:bam.h faidx.h
+sam_header.o:sam_header.h khash.h
+bcf.o:bcftools/bcf.h
+bam2bcf.o:bam2bcf.h errmod.h bcftools/bcf.h
+bam2bcf_indel.o:bam2bcf.h
+errmod.o:errmod.h
+phase.o:bam.h khash.h ksort.h
+bamtk.o:bam.h
+
+faidx.o:faidx.h razf.h khash.h
+faidx_main.o:faidx.h razf.h
+
+
+libbam.1.dylib-local:$(LOBJS)
+		libtool -dynamic $(LOBJS) -o libbam.1.dylib -lc -lz
+
+libbam.so.1-local:$(LOBJS)
+		$(CC) -shared -Wl,-soname,libbam.so -o libbam.so.1 $(LOBJS) -lc -lz
+
+dylib:
+		@$(MAKE) cleanlocal; \
+		case `uname` in \
+			Linux) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.so.1-local;; \
+			Darwin) $(MAKE) CFLAGS="$(CFLAGS) -fPIC" libbam.1.dylib-local;; \
+			*) echo 'Unknown OS';; \
+		esac
+
+
+cleanlocal:
+		rm -fr gmon.out *.o a.out *.exe *.dSYM razip bgzip $(PROG) *~ *.a *.so.* *.so *.dylib
+
+clean:cleanlocal-recur