a program to output a nonredundant list of readss

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

diff --git a/src/fastq-sw.h b/src/fastq-sw.h
deleted file mode 100644 (file)
index 6e35a77..0000000
--- a/src/fastq-sw.h
+++ /dev/null
@@ -1,39 +0,0 @@
-/*
- * 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
-