+# The default version string in bam.h and bcftools/bcf.h can be overriden directly
+# make VERSION="-DVERSION='\\\"my-version\\\"'"
+# or using the git-stamp rule
+# make git-stamp
+VERSION=
+
CC= gcc
-CFLAGS= -g -Wall -O2
+CFLAGS= -g -Wall $(VERSION) -O2
#LDFLAGS= -Wl,-rpath,\$$ORIGIN/../lib
DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1
KNETFILE_O= knetfile.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
+ 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= -lcurses # -lXCurses
+
.SUFFIXES:.c .o
.PHONY: all lib
all:$(PROG)
+git-stamp:
+ make VERSION="-DVERSION='\\\"`git describe --always --dirty`\\\"'"
+
.PHONY:all lib clean cleanlocal
.PHONY:all-recur lib-recur clean-recur cleanlocal-recur install-recur
$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) libbam.a -Lbcftools -lbcf $(LIBPATH) $(LIBCURSES) -lm -lz -lpthread
razip:razip.o razf.o $(KNETFILE_O)
- $(CC) $(CFLAGS) -o $@ razf.o razip.o $(KNETFILE_O) -lz
+ $(CC) $(CFLAGS) -o $@ $^ -lz
bgzip:bgzip.o bgzf.o $(KNETFILE_O)
- $(CC) $(CFLAGS) -o $@ bgzf.o bgzip.o $(KNETFILE_O) -lz -lpthread
+ $(CC) $(CFLAGS) -o $@ $^ -lz -lpthread
bgzf.o:bgzf.c bgzf.h
$(CC) -c $(CFLAGS) $(DFLAGS) -DBGZF_CACHE $(INCLUDES) bgzf.c -o $@
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.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