ipmatcher rule_id -> long long & scanner engine centralization

scanner/interval_matcher/cgranges.h

@@ -0,0 +1,103 @@
+/* The MIT License
+
+   Copyright (c) 2019 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 CRANGES_H
+#define CRANGES_H
+
+#include <stdint.h>
+
+#include "interval_matcher.h"
+
+typedef struct interval_result user_label_t;
+
+typedef struct {    // a contig
+	char *name;     // name of the contig
+	int32_t len;    // max length seen in data
+	int32_t root_k;
+	int64_t n, off; // sum of lengths of previous contigs
+} cr_ctg_t;
+
+typedef struct {    // an interval
+	// uint64_t x;     // prior to cr_index(), x = ctg_id<<32|start_pos; after: x = start_pos<<32|end_pos
+	// uint32_t y:31, rev:1;
+   uint64_t x;
+   uint64_t y;
+   uint64_t real_y;
+	user_label_t label;  // NOT used
+} cr_intv_t;
+
+typedef struct {
+	int64_t n_r, m_r;     // number and max number of intervals
+	cr_intv_t *r;         // list of intervals (of size _n_r_)
+	// int32_t n_ctg, m_ctg; // number and max number of contigs
+	// cr_ctg_t ctg;        // list of contigs (of size _n_ctg_)
+	// void *hc;             // dictionary for converting contig names to integers
+
+   uint64_t len;    // max length seen in data
+	int64_t root_k;
+} cgranges_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+// retrieve start and end positions from a cr_intv_t object
+// static inline int32_t cr_st(const cr_intv_t *r) { return (int32_t)(r->x>>32); }
+// static inline int32_t cr_en(const cr_intv_t *r) { return (int32_t)r->x; }
+static inline uint64_t cr_st(const cr_intv_t *r) { return r->x; }
+static inline uint64_t cr_en(const cr_intv_t *r) { return r->real_y; }
+static inline uint64_t cr_start(const cgranges_t *cr, int64_t i) { return cr_st(&cr->r[i]); }
+static inline uint64_t cr_end(const cgranges_t *cr, int64_t i) { return cr_en(&cr->r[i]); }
+static inline user_label_t cr_label(const cgranges_t *cr, int64_t i) { return cr->r[i].label; }
+
+// Initialize
+cgranges_t *cr_init(void);
+
+// Deallocate
+void cr_destroy(cgranges_t *cr);
+
+// Add an interval
+// cr_intv_t *cr_add(cgranges_t *cr, const char *ctg, int32_t st, int32_t en, user_label_t label);
+cr_intv_t *cr_add(cgranges_t *cr, uint64_t st, uint64_t en, user_label_t label);
+
+// Sort and index intervals
+void cr_index(cgranges_t *cr);
+
+// int64_t cr_overlap(const cgranges_t *cr, const char *ctg, int32_t st, int32_t en, int64_t **b_, int64_t *m_b_);
+// int64_t cr_contain(const cgranges_t *cr, const char *ctg, int32_t st, int32_t en, int64_t **b_, int64_t *m_b_);
+
+int64_t cr_overlap(const cgranges_t *cr, uint64_t st, uint64_t en, int64_t **b_, int64_t *m_b_);
+int64_t cr_contain(const cgranges_t *cr, const char *ctg, int32_t st, int32_t en, int64_t **b_, int64_t *m_b_);
+
+// Add a contig and length. Call this for desired contig ordering. _len_ can be 0.
+int32_t cr_add_ctg(cgranges_t *cr, const char *ctg, int32_t len);
+
+// Get the contig ID given its name
+int32_t cr_get_ctg(const cgranges_t *cr, const char *ctg);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif