* samtools-0.1.3-7 (r246)

[samtools.git] / Makefile.am

diff --git a/Makefile.am b/Makefile.am
new file mode 100644 (file)
index 0000000..e2304f7
--- /dev/null
+++ b/Makefile.am
@@ -0,0 +1,56 @@
+EXTRA_DIST = autogen.sh 
+bin_PROGRAMS = bgzip samtools razip
+SUBDIRS = . misc
+
+bgzip_SOURCES = bgzip.c bgzf.c
+bgzip_LDADD = -lm -lz
+
+samtools_SOURCES = bamtk.c bam.c bam_aux.c bam_import.c bam_index.c \
+                                  bam_lpileup.c bam_maqcns.c bam_mate.c bam_md.c bam_pileup.c \
+                                  bam_plcmd.c bam_rmdup.c bam_sort.c bam_stat.c \
+                                  bam_tview.c bgzf.c faidx.c glf.c kstring.c razf.c \
+                                  bam.h bam_endian.h bam_maqcns.h bgzf.h faidx.h glf.h \
+                                  khash.h kseq.h kstring.h ksort.h razf.h zutil.h
+samtools_LDADD = -lm -lz -lcurses
+
+razip_SOURCES = razip.c razf.c
+razip_LDADD = -lm -lz
+dist_bin_SCRIPTS = bowtie2sam.pl export2sam.pl novo2sam.pl samtools.pl soap2sam.pl wgsim_eval.pl zoom2sam.pl
+bin_PROGRAMS = faidx maq2sam-short maq2sam-long md5fa md5sum-lite wgsim
+
+faidx_SOURCES = ../faidx.c ../faidx.c
+#faidx_LDFLAGS = -D_NO_RAZF -DFAIDX_MAIN 
+
+md5fa_SOURCES = md5.c md5.h md5fa.c ../kseq.h
+#md5fa_LDADD = -lz
+
+md5sum_lite_SOURCES = md5.c md5.h
+#md5sum_lite_LDFLAGS = -DMD5SUM_MAIN
+
+maq2sam_short_SOURCES = maq2sam.c
+#maq2sam_short_LDADD = -lz
+
+maq2sam_long_SOURCES = maq2sam.c
+#maq2sam_long_LDADD = -lz
+
+wgsim_SOURCES = wgsim.c 
+wgsim_LDADD = -lm 
+
+faidx:../faidx.c ../faidx.h
+       $(CC) $(CFLAGS) -D_NO_RAZF -DFAIDX_MAIN -o $@ ../faidx.c
+md5fa:md5.o md5fa.o md5.h ../kseq.h
+       $(CC) $(CFLAGS) -o $@ md5.o md5fa.o -lz
+md5fa.o:md5.h md5fa.c
+       $(CC) $(CFLAGS) -c -I.. -o $@ md5fa.c
+md5sum-lite:md5sum-lite.o
+       $(CC) $(CFLAGS) -o $@ md5sum-lite.o
+md5sum-lite.o:md5.c md5.h
+       $(CC) -c $(CFLAGS) -DMD5SUM_MAIN -o $@ md5.c
+maq2sam-short:maq2sam-short.o
+       $(CC) $(CFLAGS) -o $@ maq2sam-short.o -lz 
+maq2sam-short.o:maq2sam.c
+       $(CC) -c $(CFLAGS) -o $@ maq2sam.c 
+maq2sam-long:maq2sam-long.o
+       $(CC) $(CFLAGS) -o $@ maq2sam-long.o -lz 
+maq2sam-long.o:maq2sam.c
+       $(CC) -c $(CFLAGS) -DMAQ_LONGREADS -D_MAQ_LONGREADS -o $@ maq2sam.c