diff spp/src/maqmap.h @ 6:ce08b0efa3fd draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/spp/src/maqmap.h	Tue Nov 27 16:11:40 2012 -0500
@@ -0,0 +1,70 @@
+#ifndef MAQMAP_H_
+#define MAQMAP_H_
+
+#ifdef MAQ_LONGREADS
+#  define MAX_READLEN 128
+#else
+#  define MAX_READLEN 64
+#endif
+
+#define MAX_NAMELEN 36
+#define MAQMAP_FORMAT_OLD 0
+#define MAQMAP_FORMAT_NEW -1
+
+#define PAIRFLAG_FF      0x01
+#define PAIRFLAG_FR      0x02
+#define PAIRFLAG_RF      0x04
+#define PAIRFLAG_RR      0x08
+#define PAIRFLAG_PAIRED  0x10
+#define PAIRFLAG_DIFFCHR 0x20
+#define PAIRFLAG_NOMATCH 0x40
+#define PAIRFLAG_SW      0x80
+
+#include <string.h>
+#include <zlib.h>
+#include "const.h"
+
+/*
+  name: read name
+  size: the length of the read
+  seq: read sequence (see also below)
+  seq[MAX_READLEN-1]: single end mapping quality (equals to map_qual if not paired)
+  map_qual: the final mapping quality
+  alt_qual: the lower quality of the two ends (equals to map_qual if not paired)
+  flag: status of the pair
+  dist: offset of the mate (zero if not paired)
+  info1: mismatches in the 24bp (higher 4 bits) and mismatches (lower 4 bits)
+  info2: sum of errors of the best hit
+  c[2]: count of all 0- and 1-mismatch hits on the reference
+ */
+typedef struct
+{
+	bit8_t seq[MAX_READLEN]; /* the last base is the single-end mapping quality. */
+	bit8_t size, map_qual, info1, info2, c[2], flag, alt_qual;
+	bit32_t seqid, pos;
+	int dist;
+	char name[MAX_NAMELEN];
+} maqmap1_t;
+
+typedef struct
+{
+	int format, n_ref;
+	char **ref_name;
+	bit64_t n_mapped_reads;
+	maqmap1_t *mapped_reads;
+} maqmap_t;
+
+#define maqmap_read1(fp, m1) gzread((fp), (m1), sizeof(maqmap1_t))
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+	maqmap_t *maq_new_maqmap();
+	void maq_delete_maqmap(maqmap_t *mm);
+	void maqmap_write_header(gzFile fp, const maqmap_t *mm);
+	maqmap_t *maqmap_read_header(gzFile fp);
+#ifdef __cplusplus
+}
+#endif
+
+#endif