updated ksw

ksw2.h

@@ -0,0 +1,32 @@
+#ifndef KSW2_H_
+#define KSW2_H_
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/**
+ * Global alignment with moving a band
+ *
+ * @param km        memory pool, when used with kalloc
+ * @param qlen      query length
+ * @param query     query sequence with 0 <= query[i] < m
+ * @param tlen      target length
+ * @param target    target sequence with 0 <= target[i] < m
+ * @param m         number of residue types
+ * @param mat       m*m scoring mattrix in one-dimension array
+ * @param gapo      gap open penalty; a gap of length l cost "-(gapo+l*gape)"
+ * @param gape      gap extension penalty
+ * @param w         band width
+ * @param n_cigar   (out) number of CIGAR elements
+ * @param cigar     (out) BAM-encoded CIGAR; caller need to deallocate with kfree(km, )
+ *
+ * @return          score of the alignment
+ */
+int ksw_global(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *n_cigar_, uint32_t **cigar_);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif