New command: obi ecopcr

src/libecoPCR/ecoPCR.h

@@ -0,0 +1,128 @@
+#ifndef ECOPCR_H_
+#define ECOPCR_H_
+
+#include <stdio.h>
+#include <inttypes.h>
+
+#include "../obidmscolumn.h"
+#include "../obiview.h"
+#include "../obitypes.h"
+
+#ifndef H_apat
+#include "./libapat/apat.h"
+#endif
+
+/*****************************************************
+ * 
+ *  Data type declarations
+ * 
+ *****************************************************/
+
+/*
+ * 
+ *  Sequence types
+ * 
+ */
+
+typedef struct {
+	
+	int32_t  taxid;
+	char     AC[20];
+	int32_t  DE_length;
+	int32_t  SQ_length;
+	int32_t  CSQ_length;
+	
+	char     data[1];
+	
+} ecoseqformat_t;
+
+typedef struct {
+	int32_t taxid;
+	int32_t SQ_length;
+	char    *AC;
+	char    *DE;
+	char    *SQ;
+} ecoseq_t;
+
+ 
+/*****************************************************
+ * 
+ *  Function declarations
+ * 
+ *****************************************************/
+
+/*
+ * 
+ * Low level system functions
+ * 
+ */
+
+int32_t is_big_endian();
+int32_t swap_int32_t(int32_t);
+
+void   *eco_malloc(int32_t chunksize,
+                   const char *error_message,
+                   const char *filename,
+                   int32_t    line);
+                   
+                   
+void   *eco_realloc(void *chunk,
+                    int32_t chunksize,
+                    const char *error_message,
+                    const char *filename,
+                    int32_t    line);
+                    
+void    eco_free(void *chunk,
+                 const char *error_message,
+                 const char *filename,
+                 int32_t    line);
+                 
+void    eco_trace_memory_allocation();
+void    eco_untrace_memory_allocation();
+
+#define ECOMALLOC(size,error_message) \
+	    eco_malloc((size),(error_message),__FILE__,__LINE__)
+	   
+#define ECOREALLOC(chunk,size,error_message) \
+        eco_realloc((chunk),(size),(error_message),__FILE__,__LINE__)
+        
+#define ECOFREE(chunk,error_message) \
+        eco_free((chunk),(error_message),__FILE__,__LINE__)
+        
+
+/*
+ * 
+ * Error management
+ * 
+ */
+ 
+  
+void ecoError(int32_t,const char*,const char *,int);
+
+#define ECOERROR(code,message) ecoError((code),(message),__FILE__,__LINE__)
+
+#define ECO_IO_ERROR       (1)
+#define ECO_MEM_ERROR      (2)
+#define ECO_ASSERT_ERROR   (3)
+#define ECO_NOTFOUND_ERROR (4)
+
+
+/*
+ * 
+ * Low level Disk access functions
+ * 
+ */
+
+
+int32_t    delete_apatseq(SeqPtr pseq);
+PatternPtr buildPattern(const char *pat, int32_t error_max);
+PatternPtr complementPattern(PatternPtr pat);
+
+SeqPtr ecoseq2apatseq(char* sequence, SeqPtr out, int32_t circular);
+
+char *ecoComplementPattern(char *nucAcSeq);
+char *ecoComplementSequence(char *nucAcSeq);
+char *getSubSequence(char* nucAcSeq,int32_t begin,int32_t end);
+
+
+#endif /*ECOPCR_H_*/