From b8b56b762fd46b96ef178a828d485e076fa25f38 Mon Sep 17 00:00:00 2001
From: Adam Kiezun <akiezun@broadinstitute.org>
Date: Tue, 10 May 2016 22:37:10 -0400
Subject: [PATCH] fix make java, add gitignore

---
 src/.gitignore | 12 ++++++++++++
 src/Makefile   |  2 +-
 2 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 src/.gitignore

diff --git a/src/.gitignore b/src/.gitignore
new file mode 100644
index 0000000..c0117fa
--- /dev/null
+++ b/src/.gitignore
@@ -0,0 +1,12 @@
+*.*~
+example_c
+example_cpp
+libssw.so
+libsswjni.so
+ssw.jar
+ssw.o
+ssw/Aligner.class
+ssw/Alignment.class
+ssw/Example.class
+ssw_cpp.o
+ssw_test 
diff --git a/src/Makefile b/src/Makefile
index 3c02692..f726378 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -41,7 +41,7 @@ $(JAVA_JAR): $(JAVA_OBJ)
 	jar cvfe $@ ssw.Example $^
 
 %.class: %.java
-	javac $<
+	javac -cp ./ $<
 	
 ssw.o: ssw.c ssw.h
 	$(CC) -c -o $@ $< $(CFLAGS)