Merge pull request #11 from broadinstitute/vrr_update_bwa_commit

Update to the new Apache2 branch head commit (cb950614ce72).
broadinstitute · Aug 14, 2017 · bf22f4a · bf22f4a
2 parents 7c053c9 + fafdbd2
commit bf22f4a
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Showing 3 changed files with 23 additions and 115 deletions.
diff --git a/src/main/c/Makefile b/src/main/c/Makefile
@@ -14,17 +14,17 @@ else
 LIB_EXT=Linux.so
 endif
 
-BWA_MEM_COMMIT=ec85a563e64710e7fc8c8c0b373d80570e245bd1
+BWA_MEM_COMMIT=cb950614ce7217788780b9a8d445c64cd4d8f62e
 JNI_BASE_NAME=org_broadinstitute_hellbender_utils_bwa_BwaMemIndex
 
 all: libbwa.$(LIB_EXT)
 
-libbwa.$(LIB_EXT): $(JNI_BASE_NAME).o jnibwa.o bwtidxbuild.o bwa/libbwa.a
+libbwa.$(LIB_EXT): $(JNI_BASE_NAME).o jnibwa.o bwa/libbwa.a
 	$(CC) -ggdb -dynamiclib -shared -o $@ $^ -lm -lz -lpthread
 
 bwa:
 	git clone https://github.com/lh3/bwa && cd bwa && git checkout $(BWA_MEM_COMMIT) && echo '#define BWA_COMMIT "'$(BWA_MEM_COMMIT)'"' > bwa_commit.h
-	sed -i .bak 's/\(LOBJS=.*\)/\1 $$(AOBJS)/g' bwa/Makefile
+	sed -i.bak -e's/\(LOBJS=.*\)/\1 bwtindex.o rle.o rope.o bwt.o is.o/g' bwa/Makefile
 
 bwa/libbwa.a: bwa
 	$(MAKE) CFLAGS="$(CFLAGS)" -C bwa libbwa.a
@@ -33,8 +33,6 @@ $(JNI_BASE_NAME).o: $(JNI_BASE_NAME).c jnibwa.h bwa
 
 jnibwa.o: jnibwa.c jnibwa.h bwa
 
-bwtidxbuild.o: bwtidxbuild.c bwa
-
 clean:
 	rm -rf bwa *.o *.$(LIB_EXT)
 

diff --git a/src/main/c/bwtidxbuild.c b/src/main/c/bwtidxbuild.c
diff --git a/src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c b/src/main/c/org_broadinstitute_hellbender_utils_bwa_BwaMemIndex.c
@@ -12,17 +12,31 @@ char * jstring_to_chars(JNIEnv* env, jstring in) {
     return res;
 }
 
+jint throwIllegalArgumentException(JNIEnv* env, char* message) {
+   jclass iaeClass = (*env)->FindClass(env, "java/lang/IllegalArgumentException");
+   return (*env)->ThrowNew(env, iaeClass, message);
+}
 
 JNIEXPORT jboolean JNICALL
 Java_org_broadinstitute_hellbender_utils_bwa_BwaMemIndex_createReferenceIndex( JNIEnv* env, jclass cls, jstring jReferenceFileName, jstring jIndexPrefix, jstring jAlgoName) {
 
-    extern int bwt_idx_build(const char*, const char*, const char*);
+	char *reference_file_name = jstring_to_chars(env, jReferenceFileName);
+	char *index_prefix = jstring_to_chars(env, jIndexPrefix);
+	char *algo_name = jstring_to_chars(env, jAlgoName);
+	int algo_type;
+	if (strcmp(algo_name, "auto") == 0) algo_type = 0;
+	else if (strcmp(algo_name, "is") == 0) algo_type = 3;
+	else if (strcmp(algo_name, "rb2") == 0) algo_type = 1;
+	else {
+	    char* message = malloc(sizeof(char) * (strlen(algo_name) + 100));
+	    sprintf(message, "wrong algorithm name '%s'", algo_name);
+	    throwIllegalArgumentException(env, message);
+	    free(message);
+	    return 0;
+	}
+	jboolean res = !bwa_idx_build( reference_file_name, index_prefix, algo_type, -1);
+	free(reference_file_name); free(index_prefix); free(algo_name);
 
-	char *referenceFileName = jstring_to_chars(env, jReferenceFileName);
-	char *indexPrefix = jstring_to_chars(env, jIndexPrefix);
-	char *algoName = jstring_to_chars(env, jAlgoName);
-	jboolean res = !bwt_idx_build( referenceFileName, indexPrefix, algoName);
-	free(referenceFileName); free(indexPrefix); free(algoName);
 	return res;
 }