From be1c7e50e1e8809ea56f2c9d472eccd8ffd73a97 Mon Sep 17 00:00:00 2001
From: Daniel Baumann <daniel.baumann@progress-linux.org>
Date: Fri, 19 Apr 2024 04:57:58 +0200
Subject: Adding upstream version 1.44.3.

Signed-off-by: Daniel Baumann <daniel.baumann@progress-linux.org>
---
 web/server/h2o/libh2o/deps/klib/ksw.h | 72 +++++++++++++++++++++++++++++++++++
 1 file changed, 72 insertions(+)
 create mode 100644 web/server/h2o/libh2o/deps/klib/ksw.h

(limited to 'web/server/h2o/libh2o/deps/klib/ksw.h')

diff --git a/web/server/h2o/libh2o/deps/klib/ksw.h b/web/server/h2o/libh2o/deps/klib/ksw.h
new file mode 100644
index 00000000..5162dc03
--- /dev/null
+++ b/web/server/h2o/libh2o/deps/klib/ksw.h
@@ -0,0 +1,72 @@
+#ifndef __AC_KSW_H
+#define __AC_KSW_H
+
+#include <stdint.h>
+
+#define KSW_XBYTE  0x10000
+#define KSW_XSTOP  0x20000
+#define KSW_XSUBO  0x40000
+#define KSW_XSTART 0x80000
+
+struct _kswq_t;
+typedef struct _kswq_t kswq_t;
+
+typedef struct {
+	int score; // best score
+	int te, qe; // target end and query end
+	int score2, te2; // second best score and ending position on the target
+	int tb, qb; // target start and query start
+} kswr_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+	/**
+	 * Aligning two sequences
+	 *
+	 * @param qlen    length of the query sequence (typically <tlen)
+	 * @param query   query sequence with 0 <= query[i] < m
+	 * @param tlen    length of the target sequence
+	 * @param target  target sequence
+	 * @param m       number of residue types
+	 * @param mat     m*m scoring matrix in one-dimention array
+	 * @param gapo    gap open penalty; a gap of length l cost "-(gapo+l*gape)"
+	 * @param gape    gap extension penalty
+	 * @param xtra    extra information (see below)
+	 * @param qry     query profile (see below)
+	 *
+	 * @return        alignment information in a struct; unset values to -1
+	 *
+	 * When xtra==0, ksw_align() uses a signed two-byte integer to store a
+	 * score and only finds the best score and the end positions. The 2nd best
+	 * score or the start positions are not attempted. The default behavior can
+	 * be tuned by setting KSW_X* flags:
+	 *
+	 *   KSW_XBYTE:  use an unsigned byte to store a score. If overflow occurs,
+	 *               kswr_t::score will be set to 255
+	 *
+	 *   KSW_XSUBO:  track the 2nd best score and the ending position on the
+	 *               target if the 2nd best is higher than (xtra&0xffff)
+	 *
+	 *   KSW_XSTOP:  stop if the maximum score is above (xtra&0xffff)
+	 *
+	 *   KSW_XSTART: find the start positions
+	 *
+	 * When *qry==NULL, ksw_align() will compute and allocate the query profile
+	 * and when the function returns, *qry will point to the profile, which can
+	 * be deallocated simply by free(). If one query is aligned against multiple
+	 * target sequences, *qry should be set to NULL during the first call and
+	 * freed after the last call. Note that qry can equal 0. In this case, the
+	 * query profile will be deallocated in ksw_align().
+	 */
+	kswr_t ksw_align(int qlen, uint8_t *query, int tlen, uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int xtra, kswq_t **qry);
+
+	int ksw_extend(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int h0, int *_qle, int *_tle);
+	int ksw_global(int qlen, const uint8_t *query, int tlen, const uint8_t *target, int m, const int8_t *mat, int gapo, int gape, int w, int *_n_cigar, uint32_t **_cigar);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif
-- 
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