minibwa 0.0.0

data/ext/minibwa/minibwa/bseq.h

@@ -0,0 +1,45 @@
+#ifndef MB_BSEQ_H
+#define MB_BSEQ_H
+
+#include <stdint.h>
+#include <string.h>
+#include "kommon.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+struct mb_bseq_file_s;
+typedef struct mb_bseq_file_s mb_bseq_file_t;
+
+typedef struct {
+	uint64_t l_seq, id; // FIXME: bseq doesn't fully support 64-bit integers yet
+	char *name, *seq, *qual, *comment;
+} mb_bseq1_t;
+
+mb_bseq_file_t *mb_bseq_open(const char *fn);
+void mb_bseq_close(mb_bseq_file_t *fp);
+mb_bseq1_t *mb_bseq_read(mb_bseq_file_t *fp, int64_t chunk_size, int with_qual, int with_comment, int frag_mode, int min_cnt, int64_t max_chunk_size, int *n_);
+mb_bseq1_t *mb_bseq_read_frag(int n_fp, mb_bseq_file_t **fp, int64_t chunk_size, int with_qual, int with_comment, int *n_);
+int mb_bseq_eof(mb_bseq_file_t *fp);
+
+static inline int mb_qname_len(const char *s)
+{
+	int l;
+	l = strlen(s);
+	return l >= 3 && s[l-1] >= '0' && s[l-1] <= '9' && s[l-2] == '/'? l - 2 : l;
+}
+
+static inline int mb_qname_same(const char *s1, const char *s2)
+{
+	int l1, l2;
+	l1 = mb_qname_len(s1);
+	l2 = mb_qname_len(s2);
+	return (l1 == l2 && strncmp(s1, s2, l1) == 0);
+}
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif