Merge commit 'upstream/0.5'

[pysam.git] / samtools / errmod.h

diff --git a/samtools/errmod.h b/samtools/errmod.h
new file mode 100644 (file)
index 0000000..32c07b6
--- /dev/null
+++ b/samtools/errmod.h
@@ -0,0 +1,24 @@
+#ifndef ERRMOD_H
+#define ERRMOD_H
+
+#include <stdint.h>
+
+struct __errmod_coef_t;
+
+typedef struct {
+       double depcorr;
+       struct __errmod_coef_t *coef;
+} errmod_t;
+
+errmod_t *errmod_init(float depcorr);
+void errmod_destroy(errmod_t *em);
+
+/*
+       n: number of bases
+       m: maximum base
+       bases[i]: qual:6, strand:1, base:4
+       q[i*m+j]: phred-scaled likelihood of (i,j)
+ */
+int errmod_cal(const errmod_t *em, int n, int m, uint16_t *bases, float *q);
+
+#endif