reimplemented smith-waterman

[fastq-tools.git] / src / fastq-sw.h

diff --git a/src/fastq-sw.h b/src/fastq-sw.h
new file mode 100644 (file)
index 0000000..6e35a77
--- /dev/null
+++ b/src/fastq-sw.h
@@ -0,0 +1,39 @@
+/*
+ * This file is part of fastq-tools.
+ *
+ * Copyright (c) 2011 by Daniel C. Jones <dcjones@cs.washington.edu>
+ *
+ * fastq-sw :
+ * Local alignments of nucleotide sequences via Smith-Waterman.
+ *
+ */
+
+#ifndef FASTQ_TOOLS_SW_H
+#define FASTQ_TOOLS_SW_H
+
+
+typedef struct
+{
+    unsigned char* subject;
+    int size;
+
+    int d[25];      /* cost matrix */
+    int gap_open;   /* gap open    */
+    int gap_extend; /* gap extend  */
+
+    /* matrix rows, used internally */
+    int* work0;
+    int* work1;
+
+} sw_t;
+
+/* convert a n ASCII nucleotide sequence to one suitable for fastq_sw */
+void fastq_sw_conv_seq(unsigned char*, int n);
+
+sw_t* fastq_alloc_sw(const unsigned char *subject, int size);
+void  fastq_free_sw(sw_t*);
+
+int fastq_sw(sw_t*, const unsigned char* query, int size);
+
+#endif
+