diff srf2fastq/io_lib-1.12.2/io_lib/sff.h @ 0:d901c9f41a6a default tip

Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/srf2fastq/io_lib-1.12.2/io_lib/sff.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,87 @@
+#ifndef _SFF_H_
+#define _SFF_H_
+
+#include "io_lib/Read.h"
+#include "io_lib/os.h"
+#include "io_lib/mFILE.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * This mirrors the order that the SFF header has on disc. We have one of
+ * these only.
+ *
+ * The flow and key are variable length fields as defined by flow_len
+ * and key_len.
+ * The on-disc structure is then also padded out with zeros to the 8-byte
+ * word boundary.
+ */
+typedef struct {
+    uint32_t magic;
+    char      version[4];
+    uint64_t  index_offset;
+    uint32_t  index_len;
+    uint32_t  nreads;
+    uint16_t  header_len;
+    uint16_t  key_len;
+    uint16_t  flow_len;
+    uint8_t   flowgram_format;
+    char     *flow;
+    char     *key;
+} sff_common_header;
+
+#define SFF_MAGIC   0x2e736666 /* ".sff" */
+#define SFF_VERSION "\0\0\0\1"
+
+/*
+ * We have one read_header per "reading" in the SFF archive.
+ * It too is padded to an 8-byte boundary.
+ */
+typedef struct {
+    uint16_t  header_len;
+    uint16_t  name_len;
+    uint32_t  nbases;
+    uint16_t  clip_qual_left;
+    uint16_t  clip_qual_right;
+    uint16_t  clip_adapter_left;
+    uint16_t  clip_adapter_right;
+    char     *name;
+} sff_read_header;
+
+/*
+ * We have one read_data section per reading, following the read_header.
+ * It is padded to an 8-byte boundary.
+ */
+typedef struct {
+    uint16_t *flowgram;   /* x 100.0 */
+    uint8_t  *flow_index; /* relative to last */
+    char     *bases;
+    uint8_t  *quality;
+} sff_read_data;
+
+
+/*
+ * Low level functions to decode SFF internals
+ */
+sff_common_header *decode_sff_common_header(unsigned char *buf);
+sff_common_header *read_sff_common_header(mFILE *mf);
+void free_sff_common_header(sff_common_header *h);
+sff_read_header *decode_sff_read_header(unsigned char *buf);
+void free_sff_read_header(sff_read_header *h);
+sff_read_header *read_sff_read_header(mFILE *mf);
+void free_sff_read_data(sff_read_data *d);
+sff_read_data *read_sff_read_data(mFILE *mf, int nflows, int nbases);
+
+
+/*
+ * Loads the first SFF sequence from an SFF container and returns as a Read.
+ */
+Read *mfread_sff(mFILE *mf);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _SFF_H_ */