2 * This file is part of fastq-tools.
4 * Copyright (c) 2011 by Daniel C. Jones <dcjones@cs.washington.edu>
7 * Local alignments of nucleotide sequences via Smith-Waterman.
11 #ifndef FASTQ_TOOLS_SW_H
12 #define FASTQ_TOOLS_SW_H
17 unsigned char* subject;
20 int d[25]; /* cost matrix */
21 int gap_open; /* gap open */
22 int gap_extend; /* gap extend */
24 /* matrix rows, used internally */
30 /* convert a n ASCII nucleotide sequence to one suitable for fastq_sw */
31 void fastq_sw_conv_seq(unsigned char*, int n);
33 sw_t* fastq_alloc_sw(const unsigned char *subject, int size);
34 void fastq_free_sw(sw_t*);
36 int fastq_sw(sw_t*, const unsigned char* query, int size);