diff srf2fastq/io_lib-1.12.2/io_lib/ztr.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/ztr.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,155 @@
+#ifndef _ZTR_H
+#define _ZTR_H
+
+#include "io_lib/Read.h"
+#include "io_lib/deflate_interlaced.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/* The header */
+typedef struct {
+    unsigned char  magic[8];	  /* 0xae5a54520d0a1a0a (be) */
+    unsigned char  version_major; /* ZTR_VERSION_MAJOR */
+    unsigned char  version_minor; /* ZTR_VERSION_MINOR */
+} ztr_header_t;
+
+/* The ZTR magic numbers */
+#define ZTR_MAGIC   		"\256ZTR\r\n\032\n"
+#define ZTR_VERSION_MAJOR	1
+#define ZTR_VERSION_MINOR	2
+
+/*
+ * CHUNKS
+ *
+ * Chunks consist of a block length followed by the type, format and data.
+ */
+
+typedef struct {
+    uint4 type;			/* chunk type (be) */
+    uint4 mdlength;		/* length of meta data field (be) */
+    char *mdata;		/* meta data */
+    uint4 dlength;		/* length of data field (be) */
+    char *data;			/* a format byte and the data itself */
+    int   ztr_owns;		/* boolean: true if we can free (meta)data */
+} ztr_chunk_t;
+
+/* Format types */
+#define ZTR_FORM_RAW		0
+#define ZTR_FORM_RLE		1
+#define ZTR_FORM_ZLIB		2
+#define ZTR_FORM_XRLE		3
+#define ZTR_FORM_XRLE2		4
+#define ZTR_FORM_DELTA1		64
+#define ZTR_FORM_DELTA2		65
+#define ZTR_FORM_DELTA4		66
+#define ZTR_FORM_DDELTA1	67
+#define ZTR_FORM_DDELTA2	68
+#define ZTR_FORM_DDELTA4	69
+#define ZTR_FORM_16TO8		70
+#define ZTR_FORM_32TO8		71
+#define ZTR_FORM_FOLLOW1	72
+#define ZTR_FORM_CHEB445	73
+#define ZTR_FORM_ICHEB		74
+#define ZTR_FORM_LOG2		75
+#define ZTR_FORM_STHUFF	        77
+#define ZTR_FORM_QSHIFT		79
+#define ZTR_FORM_TSHIFT		80
+
+/* Converts a C string to a big-endian 4-byte int */
+#define ZTR_STR2BE(str) (((str)[0] << 24) + \
+                         ((str)[1] << 16) + \
+                         ((str)[2] <<  8) + \
+                         ((str)[3] <<  0))
+
+/* Converts a big-endian 4-byte int to a C string */
+#define ZTR_BE2STR(i,str) (((str)[0]=((i)>>24)&0xff),\
+                           ((str)[1]=((i)>>16)&0xff),\
+                           ((str)[2]=((i)>> 8)&0xff),\
+                           ((str)[3]=((i)>> 0)&0xff),\
+			   (str)[4]='\0',str)\
+
+#define ZTR_TYPE_HEADER	0xae5a5452 /* M-. Z T R */
+
+#define ZTR_TYPE_SAMP	0x53414d50
+#define ZTR_TYPE_SMP4	0x534d5034
+#define ZTR_TYPE_BASE	0x42415345
+#define ZTR_TYPE_BPOS	0x42504f53
+#define ZTR_TYPE_CNF4	0x434e4634
+#define ZTR_TYPE_CNF1	0x434e4631
+#define ZTR_TYPE_CSID	0x43534944
+#define ZTR_TYPE_TEXT	0x54455854
+#define ZTR_TYPE_CLIP	0x434c4950
+#define ZTR_TYPE_COMM	0x434f4d4d
+#define ZTR_TYPE_CR32	0x43523332
+#define ZTR_TYPE_FLWO	0x464c574f
+#define ZTR_TYPE_FLWC	0x464c5743
+#define ZTR_TYPE_HUFF   0x48554646
+#define ZTR_TYPE_REGN   0x5245474e
+
+/* A text segment consists of identifier and value */
+typedef struct {
+    char *ident; /* Pointer to identifier */
+    char *value; /* Pointer to value */
+} ztr_text_t;
+
+typedef struct {
+    int ztr_owns; /* true is ZTR is to free the data later */
+    huffman_codeset_t *codes;
+} ztr_hcode_t;
+
+/* The main ZTR structure, which holds the entire file contents */
+typedef struct {
+    /* General bits to do with the ZTR file format */
+    ztr_header_t header;	/* File Header */
+    ztr_chunk_t *chunk;		/* Array of chunks */
+    int nchunks;		/* Number of chunks */
+
+    /* Specifics to do with the standard chunk types */
+    ztr_text_t *text_segments;
+    int ntext_segments;
+
+    /* 'Hint' for delta of SAMP and SMP4 */
+    int delta_level;
+
+    /* Cached huffman encoding/decoding tables for STHUFF format */
+    ztr_hcode_t *hcodes;
+    int nhcodes;
+    int hcodes_checked;
+} ztr_t;
+
+int ztr_read_header(mFILE *fp, ztr_header_t *h);
+ztr_chunk_t *ztr_read_chunk_hdr(mFILE *fp);
+
+int fwrite_ztr(FILE *fp, ztr_t *ztr);
+int mfwrite_ztr(mFILE *fp, ztr_t *ztr);
+ztr_t *fread_ztr(FILE *fp);
+ztr_t *mfread_ztr(mFILE *fp);
+Read *ztr2read(ztr_t *ztr);
+ztr_t *read2ztr(Read *r);
+int compress_ztr(ztr_t *ztr, int level);
+int uncompress_ztr(ztr_t *ztr);
+ztr_t *new_ztr(void);
+void delete_ztr(ztr_t *ztr);
+ztr_chunk_t **ztr_find_chunks(ztr_t *ztr, uint4 type, int *nchunks_p);
+void ztr_process_text(ztr_t *ztr);
+int compress_chunk(ztr_t *ztr, ztr_chunk_t *chunk, int format,
+		   int option, int option2);
+int uncompress_chunk(ztr_t *ztr, ztr_chunk_t *chunk);
+ztr_hcode_t *ztr_add_hcode(ztr_t *ztr, huffman_codeset_t *codes, int ztr_owns);
+int ztr_store_hcodes(ztr_t *ztr);
+ztr_hcode_t *ztr_find_hcode(ztr_t *ztr, int code_set);
+ztr_chunk_t *ztr_find_hcode_chunk(ztr_t *ztr, int code_set);
+char *ztr_lookup_mdata_value(ztr_t *z, ztr_chunk_t *chunk, char *key);
+ztr_chunk_t *ztr_new_chunk(ztr_t *ztr, uint4 type,
+			   char *data,  uint4 dlength,
+			   char *mdata, uint4 mdlength);
+ztr_chunk_t *ztr_add_text(ztr_t *z, ztr_chunk_t *ch,
+			  const char *key, const char *value);
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _ZTR_H */