First commit

pkg/obiformats/fastseq_read.h

@@ -0,0 +1,41 @@
+#ifndef _READ_H
+#define _READ_H
+
+#include <zlib.h>
+#include <stdio.h>
+#include <stdint.h>
+#include <stdbool.h> 
+
+#include "kseq/kseq.h"
+
+KSEQ_INIT(gzFile, gzread)
+
+typedef struct {
+  kseq_t  *seq;
+  bool    finished;
+  int16_t shift;
+  gzFile filez;
+} fast_kseq_t, *fast_kseq_p;
+ 
+
+fast_kseq_t* open_fast_sek_file(const char* filename, int shift);
+fast_kseq_t* open_fast_sek_fd(int fd, bool keep_open, int shift);
+fast_kseq_t* open_fast_sek_stdin(int shift);
+
+/**
+ * @brief read the next sequence on the fast* stream
+ * 
+ * @param seq a kseq_t* created using function open_fast_sek
+ * @return int if greater than 0 represents the length of the
+ *             sequence, otherwise indicates an error
+ *              - -1 : no more sequence in the stream
+ *              - -2 : too short quality sequence
+ *              - -3 : called with NULL pointer
+ */ 
+int64_t next_fast_sek(fast_kseq_t* iterator);
+
+
+int close_fast_sek(fast_kseq_t* iterator);
+int rewind_fast_sek(fast_kseq_t* iterator);
+
+#endif