82 lines
2.4 KiB
C
82 lines
2.4 KiB
C
/*
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* File: scfIO.h
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*
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* Author: Simon Dear
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* MRC Laboratory of Molecular Biology
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* Hills Road
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* Cambridge CB2 2QH
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* United Kingdom
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*
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* Description: header file for SCF file IO
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*
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* Created: 8 October 1992 (from seqIOSCF.c)
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* Updated:
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*
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*/
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#ifndef _SCFIO_H_
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#define _SCFIO_H_
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#include "mach-io.h"
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/* ---- Constants ---- */
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#define SCF_MAGIC (((((uint_4)'.'<<8)+(uint_4)'s'<<8)+(uint_4)'c'<<8)+(uint_4)'f')
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/*
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** Type definition for the Header structure
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*/
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typedef struct {
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uint_4 magic_number; /* Always ((('.'<<8)+'s'<<8)+'c'<<8)+'f'; */
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uint_4 samples; /* Number of elements in Samples matrix */
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uint_4 samples_offset; /* Byte offset from start of file */
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uint_4 bases; /* Number of bases in Bases matrix */
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uint_4 bases_left_clip; /* Number of bases in left clip (vector)*/
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uint_4 bases_right_clip; /* Number of bases in right clip (unreliable) */
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uint_4 bases_offset; /* Byte offset from start of file */
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uint_4 comments_size; /* Number of bytes in Comment section */
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uint_4 comments_offset; /* Byte offset from start of file */
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uint_4 spare[23]; /* Unused */
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} Header;
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/*
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** Type definition for the Sample data
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*/
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typedef struct {
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uint_1 sample_A; /* Sample for A trace */
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uint_1 sample_C; /* Sample for C trace */
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uint_1 sample_G; /* Sample for G trace */
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uint_1 sample_T; /* Sample for T trace */
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} Samples;
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/*
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** Type definition for the sequence data
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*/
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typedef struct {
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uint_4 peak_index; /* Index into Samples matrix for base position */
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uint_1 prob_A; /* Probability of it being an A */
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uint_1 prob_C; /* Probability of it being an C */
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uint_1 prob_G; /* Probability of it being an G */
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uint_1 prob_T; /* Probability of it being an T */
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uint_1 base; /* Base called */
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uint_1 spare[3]; /* Spare */
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} Bases;
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/*
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** Type definition for the comments
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*/
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typedef char Comments; /* Zero terminated list of \n separated entries */
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extern int read_scf_header(FILE *fp, Header *h);
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extern int read_scf_sample(FILE *fp, Samples *s);
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extern int read_scf_base(FILE *fp, Bases *b);
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extern int write_scf_header(FILE *fp, Header *h);
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extern int write_scf_sample(FILE *fp, Samples *s);
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extern int write_scf_base(FILE *fp, Bases *b);
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extern int write_scf_comment(FILE *fp, Comments *c, size_t l);
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#endif /*_SCFIO_H_*/
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