ruby-minigraph 0.0.20.0

data/ext/minigraph/miniwfa.h

@@ -0,0 +1,95 @@
+/*
+  The MIT License
+
+  Copyright (c) 2022-     Dana-Farber Cancer Institute
+
+  Permission is hereby granted, free of charge, to any person obtaining
+  a copy of this software and associated documentation files (the
+  "Software"), to deal in the Software without restriction, including
+  without limitation the rights to use, copy, modify, merge, publish,
+  distribute, sublicense, and/or sell copies of the Software, and to
+  permit persons to whom the Software is furnished to do so, subject to
+  the following conditions:
+
+  The above copyright notice and this permission notice shall be
+  included in all copies or substantial portions of the Software.
+
+  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+  NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+  BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+  ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+  CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+  SOFTWARE.
+*/
+
+#ifndef MINIWFA_H
+#define MINIWFA_H
+
+#include <stdint.h>
+
+#define MWF_F_CIGAR      0x1
+#define MWF_F_NO_KALLOC  0x2
+#define MWF_F_DEBUG      0x10000
+
+typedef struct {
+	int32_t flag;     // bit flag; see MWF_F_* macros
+	int32_t x, o1, e1, o2, e2; // scoring
+	int32_t step;     // distance between checkpoints in the low-memory mode
+	int32_t max_s;    // stop the alignment if score is higher than this
+	int64_t max_iter;
+	// chaining heuristics
+	int32_t max_occ, kmer, min_len;
+} mwf_opt_t;
+
+typedef struct {
+	int32_t s;       // score
+	int32_t n_cigar; // number of CIGAR operators
+	int64_t n_iter;
+	uint32_t *cigar; // CIGAR in the htslib packing: len<<4|op
+} mwf_rst_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/**
+ * Set default parameters
+ *
+ * @param opt     (out) options
+ */
+void mwf_opt_init(mwf_opt_t *opt);
+
+/**
+ * Align two sequences with WFA
+ *
+ * mwf_wfa_exact() finds the optimal alignment without heuristics.
+ *
+ * mwf_wfa_chain() does chaining and closes gaps in the chain. This is a
+ * heuristic algorithm and may miss the optimal alignment.
+ *
+ * mwf_wfa_auto() calls mwf_wfa_exact() for penalty up to 5000. If fails,
+ * it invokes mwf_wfa_chain() with a step size of 5000.
+ *
+ * @param km      kalloc handler. Set to NULL to use malloc.
+ * @param opt     parameters
+ * @param tl      target sequence length
+ * @param ts      target sequence
+ * @param ql      query sequence length
+ * @param qs      query sequence
+ * @param r       (out) results
+ */
+void mwf_wfa_exact(void *km, const mwf_opt_t *opt, int32_t tl, const char *ts, int32_t ql, const char *qs, mwf_rst_t *r);
+void mwf_wfa_chain(void *km, const mwf_opt_t *opt, int32_t tl, const char *ts, int32_t ql, const char *qs, mwf_rst_t *r);
+void mwf_wfa_auto(void *km, const mwf_opt_t *opt,  int32_t tl, const char *ts, int32_t ql, const char *qs, mwf_rst_t *r);
+
+// These functions are in "mwf-dbg.c". For debugging only.
+int32_t mwf_cigar2score(const mwf_opt_t *opt, int32_t n_cigar, const uint32_t *cigar, int32_t *tl, int32_t *ql);
+void mwf_assert_cigar(const mwf_opt_t *opt, int32_t n_cigar, const uint32_t *cigar, int32_t tl0, int32_t ql0, int32_t s0);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif