[PR] 进行了一点更新

Makefile

@@ -1,56 +1,74 @@
 CC=		gcc
-CFLAGS=		-g -Wall -O2 
-DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DBGZF_CACHE
-LOBJS=		bgzf.o kstring.o bam_aux.o bam.o bam_import.o bam_index.o sam_header.o bedutil.o commons.o
-PROG=		bamdst
-INCLUDES=	-Isamlib/ -I.
-SUBDIRS=	. samlib
-LIBPATH=        -L. 
+CFLAGS=		-g -Wall -O2 -std=gnu99
+DFLAGS=		-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE
+
+# Source files
+SOURCES=	xamdst.c kstring.c bedutil.c commons.c
+PROG=		xamdst
+
+# ---- htslib configuration ---------------------------------------------------
+# Resolution order:
+#   1. HTSLIB_DIR=<path>     explicit override (a built htslib source tree)
+#   2. system htslib         detected via pkg-config
+#   3. sibling ./htslib      local source tree -- libhts.a is auto-built if missing
+#   4. otherwise             error
+#
+# If static linking fails with "cannot find -lbz2/-llzma", your htslib was
+# built without them -- override:
+#       make HTSLIB_DEPS="-lz -lpthread -lm"
+HTSLIB_DIR ?=
+
+ifeq ($(HTSLIB_DIR),)
+  HAVE_PKG_HTSLIB := $(shell pkg-config --exists htslib 2>/dev/null && echo yes)
+  ifneq ($(HAVE_PKG_HTSLIB),)
+    # 2. system htslib (pkg-config)
+    HTSLIB_CFLAGS := $(shell pkg-config --cflags htslib)
+    HTSLIB_LIBS   := $(shell pkg-config --libs htslib)
+  else
+    ifneq ($(wildcard htslib/htslib/hts.h),)
+      # 3. sibling ./htslib source tree (libhts.a auto-built below)
+      HTSLIB_CFLAGS := -Ihtslib
+      HTSLIB_LIBS   := htslib/libhts.a
+      HTSLIB_DEPS   ?= -lz -lbz2 -llzma -lpthread -lm
+      HTSLIB_BUILD  := htslib/libhts.a
+    else
+      # 4. not found
+      $(error htslib not found. \
+Install htslib system-wide (then pkg-config detects it), \
+or clone it as a sibling: `git clone https://github.com/samtools/htslib htslib`, \
+or pass HTSLIB_DIR=/path/to/htslib)
+    endif
+  endif
+else
+  # 1. explicit override
+  HTSLIB_CFLAGS := -I$(HTSLIB_DIR)
+  HTSLIB_LIBS   := $(HTSLIB_DIR)/libhts.a
+  HTSLIB_DEPS   ?= -lz -lbz2 -llzma -lpthread -lm
+  HTSLIB_BUILD  := $(HTSLIB_DIR)/libhts.a
+endif
+
+INCLUDES=	-I. $(HTSLIB_CFLAGS)
+LIBS=		$(HTSLIB_LIBS) $(HTSLIB_DEPS) -lz -lpthread -lm
 
 .SUFFIXES:.c .o
-.PHONY: all
+.PHONY: all clean
+
+# auto-build the local htslib (handles a git clone: autoreconf + configure + make)
+ifdef HTSLIB_BUILD
+$(HTSLIB_BUILD):
+		cd $(dir $(HTSLIB_BUILD)) && \
+		(test -f configure || autoreconf -i) && \
+		(test -f config.status || ./configure) && \
+		$(MAKE)
+endif
 
 .c.o:
 		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
 
-all:clean $(PROG) 
-
-.PHONY:all  clean
-
-lib:libbam.a
-
-libbam.a:$(LOBJS)
-		$(AR) -csru $@ $(LOBJS)
-
-bamdst:lib $(AOBJS) samlib/bam.h
-		$(CC) $(CFLAGS) -o $@ $(AOBJS) $(LDFLAGS) bamdst.c $(LIBPATH) $(INCLUDES) -lm -lbam -lz
-
-bgzf.o:bgzf.c bgzf.h
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) bgzf.c -o $@
-
-kstring.o:kstring.c kstring.h
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) kstring.c -o $@
-
-bam.o:samlib/bam.h samlib/bam_endian.h kstring.h samlib/sam_header.h samlib/bam.c
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) samlib/bam.c -o $@
-
-bam_import.o:samlib/bam.h kseq.h khash.h samlib/bam_import.c
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) samlib/bam_import.c -o $@
-
-bam_index.o:samlib/bam.h khash.h ksort.h  samlib/bam_endian.h samlib/bam_index.c  
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) samlib/bam_index.c -o $@
-
-sam_header.o:samlib/sam_header.h khash.h samlib/sam_header.c
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) samlib/sam_header.c -o $@
-
-bam_aux.o:samlib/bam.h samlib/bam_aux.c khash.h
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) samlib/bam_aux.c -o $@
-
-commons.o:commons.c commons.h
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) commons.c -o $@	
+all:clean $(PROG)
 
-bedutil.o:bedutil.c bedutil.h
-		$(CC) -c $(CFLAGS) $(DFLAGS) $(INCLUDES) bedutil.c -o $@	
+xamdst: $(SOURCES:.c=.o) $(HTSLIB_BUILD)
+		$(CC) $(CFLAGS) -o $@ $(SOURCES:.c=.o) $(INCLUDES) $(LIBS)
 
 clean:
 		rm -fr gmon.out *.o a.out *.exe *.dSYM  $(PROG) *~ *.a target.dep *.plot *.report *.tsv.gz uncover.bed