129 lines
2.6 KiB
C
129 lines
2.6 KiB
C
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#ifndef ECOPCR_H_
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#define ECOPCR_H_
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#include <stdio.h>
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#include <inttypes.h>
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#include "../obidmscolumn.h"
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#include "../obiview.h"
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#include "../obitypes.h"
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#ifndef H_apat
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#include "./libapat/apat.h"
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#endif
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/*****************************************************
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*
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* Data type declarations
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*
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*****************************************************/
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/*
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*
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* Sequence types
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*
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*/
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typedef struct {
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int32_t taxid;
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char AC[20];
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int32_t DE_length;
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int32_t SQ_length;
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int32_t CSQ_length;
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char data[1];
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} ecoseqformat_t;
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typedef struct {
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int32_t taxid;
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int32_t SQ_length;
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char *AC;
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char *DE;
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char *SQ;
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} ecoseq_t;
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/*****************************************************
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*
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* Function declarations
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*
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*****************************************************/
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/*
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*
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* Low level system functions
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*
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*/
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int32_t is_big_endian();
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int32_t swap_int32_t(int32_t);
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void *eco_malloc(int32_t chunksize,
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const char *error_message,
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const char *filename,
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int32_t line);
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void *eco_realloc(void *chunk,
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int32_t chunksize,
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const char *error_message,
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const char *filename,
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int32_t line);
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void eco_free(void *chunk,
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const char *error_message,
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const char *filename,
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int32_t line);
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void eco_trace_memory_allocation();
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void eco_untrace_memory_allocation();
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#define ECOMALLOC(size,error_message) \
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eco_malloc((size),(error_message),__FILE__,__LINE__)
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#define ECOREALLOC(chunk,size,error_message) \
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eco_realloc((chunk),(size),(error_message),__FILE__,__LINE__)
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#define ECOFREE(chunk,error_message) \
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eco_free((chunk),(error_message),__FILE__,__LINE__)
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/*
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*
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* Error management
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*
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*/
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void ecoError(int32_t,const char*,const char *,int);
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#define ECOERROR(code,message) ecoError((code),(message),__FILE__,__LINE__)
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#define ECO_IO_ERROR (1)
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#define ECO_MEM_ERROR (2)
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#define ECO_ASSERT_ERROR (3)
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#define ECO_NOTFOUND_ERROR (4)
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/*
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*
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* Low level Disk access functions
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*
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*/
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int32_t delete_apatseq(SeqPtr pseq);
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PatternPtr buildPattern(const char *pat, int32_t error_max);
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PatternPtr complementPattern(PatternPtr pat);
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SeqPtr ecoseq2apatseq(char* sequence, SeqPtr out, int32_t circular);
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char *ecoComplementPattern(char *nucAcSeq);
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char *ecoComplementSequence(char *nucAcSeq);
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char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end);
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#endif /*ECOPCR_H_*/
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