X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=tabix.git;a=blobdiff_plain;f=Makefile;h=a51c1757ad139d7135da8ad42a8b71a01b66c04d;hp=3d7153d4a58bcfb8508eaef041f7f50d22e3191c;hb=c70c92b7a385548d8e670638a93a083401f49e4d;hpb=7f5c10e58cb433a02137112209d408ecb9e65751

diff --git a/Makefile b/Makefile
index 3d7153d..a51c175 100644
--- a/Makefile
+++ b/Makefile
@@ -37,6 +37,9 @@ tabix:lib $(AOBJS)
 bgzip:bgzip.o bgzf.o knetfile.o
 		$(CC) $(CFLAGS) -o $@ bgzip.o bgzf.o knetfile.o -lz
 
+TabixReader.class:TabixReader.java
+		javac -cp .:sam.jar TabixReader.java
+
 kstring.o:kstring.h
 knetfile.o:knetfile.h
 bgzf.o:bgzf.h knetfile.h
@@ -44,7 +47,10 @@ index.o:bgzf.h tabix.h khash.h ksort.h kstring.h
 main.o:tabix.h kstring.h bgzf.h
 bgzip.o:bgzf.h
 
+tabix.pdf:tabix.tex
+		pdflatex tabix.tex
+
 cleanlocal:
-		rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a
+		rm -fr gmon.out *.o a.out *.dSYM $(PROG) *~ *.a tabix.aux tabix.log tabix.pdf *.class
 
 clean:cleanlocal-recur