Unfinished

[samtools.git] / Makefile.am

diff --git a/Makefile.am b/Makefile.am
index e2304f7a849193fa1a5942903737295af4fc8d62..b55403debc288e65d49f507720d96d2df39321c8 100644 (file)
--- a/Makefile.am
+++ b/Makefile.am
@@ -7,50 +7,12 @@ 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_plcmd.c bam_rmdup.c bam_sort.c bam_stat.c bam_rmdupse.c \
+                                  bam_tview.c bgzf.c faidx.c glf.c kstring.c razf.c sam.c sam_view.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
+                                  khash.h kseq.h kstring.h ksort.h razf.h zutil.h sam.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