diff srf2fastq/io_lib-1.12.2/io_lib/Read.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/Read.h	Tue Jun 07 17:48:05 2011 -0400
@@ -0,0 +1,274 @@
+/*
+ * Copyright (c) Medical Research Council 1994. All rights reserved.
+ *
+ * Permission to use, copy, modify and distribute this software and its
+ * documentation for any purpose is hereby granted without fee, provided that
+ * this copyright and notice appears in all copies.
+ *
+ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
+ * as part of the Staden Package at the MRC Laboratory of Molecular
+ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
+ *
+ * MRC disclaims all warranties with regard to this software.
+ */
+
+#ifndef _Read_h_
+#define _Read_h_
+
+/* 
+ * Title:	Read
+ *
+ * File: 	Read.h
+ * Purpose:	Read data type
+ * Last update:	June  14 1994
+ */
+
+/*
+ * This module encodes the `Read' sequence data structure.
+ *
+ * A `Read' contains information about bases and traces which are laid
+ * out along a single dimension of points. The number of points in a
+ * paricular sequence is given by `getNPoints', and these are numbered
+ * 0..getNPoints-1. At each point there are four trace readings, one
+ * for each base.
+ *
+ * The number of bases is `getNBases' which are numbered 0..N-1. 
+ * Bases are represented by `char's. Every base is located at a 
+ * particular point.
+ *
+ * The behaviour of these routines is undefined if given NULLRead or
+ * an undefined sequence.
+ */
+
+#include "io_lib/os.h"
+#include "io_lib/scf.h"
+#include "io_lib/mFILE.h"
+
+#ifdef __cplusplus
+extern "C" {
+#endif
+
+/*
+ * The autoconf setup doesn't use options.mk as the Makefile is rebuilt.
+ * I haven't worked out how to do the analogous via autoconf, so for now
+ * I take the easy approach and hard-code all formats to be enabled
+ */
+#ifdef HAVE_CONFIG_H
+#include "io_lib_config.h"
+#define IOLIB_ABI
+#define IOLIB_SCF
+#define IOLIB_ALF
+#define IOLIB_PLN
+#define IOLIB_CTF
+#define IOLIB_EXP
+#define IOLIB_SFF
+#endif
+
+/* Only add ZTR support if we've got ZLIB installed */
+#ifdef HAVE_ZLIB
+#  ifndef IOLIB_ZTR
+#    define IOLIB_ZTR
+#  endif
+#endif
+
+/*
+ *-----------------------------------------------------------------------------
+ * Macros
+ *-----------------------------------------------------------------------------
+ */
+
+#define NULLRead     ((Read *)NULL)
+
+/* Trace file formats */
+#define TT_ERR -1
+#define TT_UNK 0
+#define TT_SCF 1
+#define TT_ABI 2
+#define TT_ALF 3
+#define TT_PLN 4
+#define TT_EXP 5
+#define TT_CTF 6
+#define TT_ZTR 7
+#define TT_ZTR1 8
+#define TT_ZTR2 9
+#define TT_ZTR3 10
+#define TT_BIO 11
+#define TT_SFF 12
+#define TT_ANY TT_UNK
+/* ANYTR is specifically any *trace* type and not EXP or PLN format */
+#define TT_ANYTR 13
+
+#define READ_BASES	(1<<0)
+#define READ_SAMPLES	(1<<1)
+#define READ_COMMENTS	(1<<2)
+#define READ_ALL	(READ_BASES | READ_SAMPLES | READ_COMMENTS)
+
+/*
+ *-----------------------------------------------------------------------------
+ * Structures and typedefs
+ *-----------------------------------------------------------------------------
+ */
+
+typedef uint_2 TRACE;        /* for trace heights */
+
+typedef struct
+{
+    int		format;	     /* Trace file format */
+    char       *trace_name;  /* Trace file name */
+
+    int         NPoints;     /* No. of points of data */
+    int         NBases;      /* No. of bases */
+
+    /* Traces */
+    TRACE      *traceA;      /* Array of length `NPoints' */
+    TRACE      *traceC;      /* Array of length `NPoints' */
+    TRACE      *traceG;      /* Array of length `NPoints' */
+    TRACE      *traceT;      /* Array of length `NPoints' */
+    TRACE       maxTraceVal; /* The maximal value in any trace */
+    int         baseline;    /* The zero offset for TRACE values */ 
+
+    /* Bases */
+    char       *base;        /* Array of length `NBases' */
+    uint_2     *basePos;     /* Array of length `NBases' */
+
+    /* Cutoffs */
+    int         leftCutoff;  /* Number of unwanted bases */
+    int         rightCutoff; /* First unwanted base at right end */
+
+    /* Miscellaneous Sequence Information */
+    char       *info;        /* misc seq info, eg comments */
+
+    /* Probability information */
+    char       *prob_A;      /* Array of length 'NBases' */
+    char       *prob_C;      /* Array of length 'NBases' */
+    char       *prob_G;      /* Array of length 'NBases' */
+    char       *prob_T;      /* Array of length 'NBases' */
+
+    /* The original input format data, or NULL if inapplicable */
+    int orig_trace_format;
+    void (*orig_trace_free)(void *ptr);
+    void *orig_trace;
+
+    char       *ident;	     /* Seq id, NULL for unknown. Malloced data.
+				Owned and freed by io_lib. */
+
+    /* Pyrosequencing "peaks" (more like spikes). NULL if not used */
+    int          nflows;     /* Number of "flows" */
+    char        *flow_order; /* Bases flowed across */
+    float       *flow;       /* Processed to be 1 base unit oriented */
+    unsigned int*flow_raw;   /* Unprocessed data */
+
+    void *private_data;	     /* The 'private data' block and size from SCF, */
+    int private_size;        /*         NULL & 0 if not present.            */
+} Read;
+
+
+/*
+ *-----------------------------------------------------------------------------
+ * Function prototypes
+ *-----------------------------------------------------------------------------
+ */
+
+
+/* ----- Main I/O routines ----- */
+
+/*
+ * Read a sequence from a file "fn" of format "format". If "format" is 0
+ * (TT_ANY), we automatically determine the correct format.
+ *
+ * Returns:
+ *   Read *   for success
+ *   NULLRead for failure
+ */
+Read *read_reading(char *fn, int format);
+Read *fread_reading(FILE *fp, char *fn, int format);
+Read *mfread_reading(mFILE *fp, char *fn, int format);
+
+
+/*
+ * Write a sequence to a file "fn" of format "format". If "format" is 0,
+ * we choose our favourite - SCF.
+ *
+ * Returns:
+ *   0 for success
+ *  -1 for failure
+ */
+int write_reading(char *fn, Read *read, int format);
+int fwrite_reading(FILE *fp, Read *read, int format);
+int mfwrite_reading(mFILE *fp, Read *read, int format);
+
+
+/* ----- Utility routines ----- */
+
+/*
+ * Allocate a new sequence, with the given sizes.
+ * Returns:
+ *   "Read *" for success
+ *   "NULLRead" for failure
+ */
+Read *read_allocate(int num_points, int num_bases);
+
+
+/*
+ * Duplicates the read structure and optionally gives it a new filename.
+ * The following fields are not duplicated:
+ *    
+ *  int  orig_trace_format;
+ *  void (*orig_trace_free)(void *ptr);
+ *  void *orig_trace;
+ *  char *ident;
+ *
+ * Returns:
+ *   "Read *" for success
+ *   "NULLRead" for failure
+ */
+Read* read_dup( Read* src, const char* new_name );
+
+
+/*
+ * Free memory allocated to a sequence by read_allocate().
+ */
+void read_deallocate(Read *read);
+
+/* unix specific file deletion routine */
+
+int remove_file(char *fn);
+
+Read *read_abi(char *fn);
+Read *fread_abi(FILE *fp);
+Read *mfread_abi(mFILE *fp);
+int write_abi(char *fn, Read *read);
+int fwrite_abi(FILE *fp, Read *read);
+int mfwrite_abi(mFILE *fp, Read *read);
+
+int write_alf(char *fn, Read *read);
+int fwrite_alf(FILE *fp, Read *read);
+int mfwrite_alf(mFILE *fp, Read *read);
+Read *read_alf(char *fn);
+Read *fread_alf(FILE *fp);
+Read *mfread_alf(mFILE *fp);
+
+int write_pln(char *fn, Read *read);
+int fwrite_pln(FILE *fp, Read *read);
+int mfwrite_pln(mFILE *fp, Read *read);
+Read *read_pln(char *fn);
+Read *fread_pln(FILE *fp);
+Read *mfread_pln(mFILE *fp);
+
+Read *read_ctf(char *fn);
+Read *fread_ctf(FILE *fp);
+Read *mfread_ctf(mFILE *fp);
+int write_ctf(char *fn, Read *read);
+int fwrite_ctf(FILE *fp, Read *read);
+int mfwrite_ctf(mFILE *fp, Read *read);
+
+int read_sections(int sec);
+
+#include "io_lib/translate.h"
+#include "io_lib/compress.h"
+
+#ifdef __cplusplus
+}
+#endif
+
+#endif /* _Read_h_ */