Mark supplementary alignments of duplicates as duplicates.

Added LZ4 for faster temporary file writing.

Makefile

@@ -29,6 +29,12 @@ CFLAGS   = -g -Wall -O2
 LDFLAGS  =
 LIBS     =
 
+LZ4DIR   = ./lz4
+LZ4_CPPFLAGS = -I$(LZ4DIR)
+LZ4_LDFLAGS  = -L$(LZ4DIR)
+
+
+
 LOBJS=      bam_aux.o bam.o bam_import.o sam.o \
             sam_header.o bam_plbuf.o
 AOBJS=      bam_index.o bam_plcmd.o sam_view.o \
@@ -38,7 +44,7 @@ AOBJS=      bam_index.o bam_plcmd.o sam_view.o \
             cut_target.o phase.o bam2depth.o padding.o bedcov.o bamshuf.o \
             faidx.o dict.o stats.o stats_isize.o bam_flags.o bam_split.o \
             bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o \
-            bam_quickcheck.o bam_addrprg.o bam_markdup.o
+            bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o
 
 prefix      = /usr/local
 exec_prefix = $(prefix)
@@ -82,11 +88,11 @@ TEST_PROGRAMS = \
 	test/split/test_filter_header_rg \
 	test/split/test_parse_args \
 	test/vcf-miniview
-
+        
 all: $(PROGRAMS) $(MISC_PROGRAMS) $(TEST_PROGRAMS)
 
-ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(CPPFLAGS)
-ALL_LDFLAGS  = $(HTSLIB_LDFLAGS) $(LDFLAGS)
+ALL_CPPFLAGS = -I. $(HTSLIB_CPPFLAGS) $(LZ4_CPPFLAGS) $(CPPFLAGS)
+ALL_LDFLAGS  = $(HTSLIB_LDFLAGS) $(LZ4_LDFLAGS) $(LDFLAGS)
 ALL_LIBS     = -lz $(LIBS)
 
 # Usually config.mk and config.h are generated by running configure
@@ -124,6 +130,11 @@ print-version:
 
 .c.o:
 	$(CC) $(CFLAGS) $(ALL_CPPFLAGS) -c -o $@ $<
+
+lz4:$(LZ4DIR)/liblz4.a
+
+$(LZ4DIR)/liblz4.a:
+	$(MAKE) -C $(LZ4DIR) liblz4.a
 
 
 LIBST_OBJS = sam_opts.o sam_utils.o
@@ -134,8 +145,8 @@ lib:libbam.a
 libbam.a:$(LOBJS)
 	$(AR) -csru $@ $(LOBJS)
 
-samtools: $(AOBJS) libbam.a libst.a $(HTSLIB)
-	$(CC) $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a libst.a $(HTSLIB_LIB) $(CURSES_LIB) -lm $(ALL_LIBS) -lpthread
+samtools: $(AOBJS) libbam.a libst.a $(HTSLIB) $(LZ4DIR)/liblz4.a
+	$(CC) $(ALL_LDFLAGS) -o $@ $(AOBJS) libbam.a libst.a $(HTSLIB_LIB) $(LZ4DIR)/liblz4.a $(CURSES_LIB) -lm $(ALL_LIBS) -lpthread
 
 # For building samtools and its test suite only: NOT to be installed.
 libst.a: $(LIBST_OBJS)
@@ -196,6 +207,7 @@ sample.o: sample.c config.h $(sample_h) $(htslib_khash_h)
 stats_isize.o: stats_isize.c config.h stats_isize.h $(htslib_khash_h)
 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)
 bam_markdup.o: bam_markdup.c config.h $(htslib_sam_h) $(sam_opts_h) samtools.h $(bam_h) $(htslib_khash_h)
+tmp_file.o: tmp_file.c config.h tmp_file.h
 
 
 # test programs
@@ -311,8 +323,11 @@ distclean: clean
 	-rm -f config.cache config.h config.log config.mk config.status
 	-rm -f TAGS
 	-rm -rf autom4te.cache
+
+lz4clean:
+	$(MAKE) -C $(LZ4DIR) clean
 
-clean-all: clean clean-htslib
+clean-all: clean clean-htslib lz4clean
 
 
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