Imported Upstream version 0.5

[pysam.git] / samtools / kprobaln.h

diff --git a/samtools/kprobaln.h b/samtools/kprobaln.h
new file mode 100644 (file)
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+++ b/samtools/kprobaln.h
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+/* The MIT License
+
+   Copyright (c) 2003-2006, 2008, 2009 by Heng Li <lh3@live.co.uk>
+
+   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 LH3_KPROBALN_H_
+#define LH3_KPROBALN_H_
+
+#include <stdint.h>
+
+typedef struct {
+       float d, e;
+       int bw;
+} kpa_par_t;
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+       int kpa_glocal(const uint8_t *_ref, int l_ref, const uint8_t *_query, int l_query, const uint8_t *iqual,
+                                  const kpa_par_t *c, int *state, uint8_t *q);
+
+#ifdef __cplusplus
+}
+#endif
+
+extern kpa_par_t kpa_par_def, kpa_par_alt;
+
+#endif