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1 #ifndef __SAM
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2 #define __SAM
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3
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4 #include <stdio.h>
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5 #include <stdlib.h>
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6 #include <string.h>
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7 #include <zlib.h>
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8 #include <dirent.h>
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9
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10 #include "globals.h"
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11 #include "utils.h"
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12
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13 void read_depth(char *, char *, char);
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14 void readSAM(char *, char *, char);
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15
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16 int insert_read_lw(char *, int, char *, int);
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17 int insert_read_sw(char *, int, char *, int);
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18 int insert_read_cw(char *, int, char *, int);
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19
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20 int findChrom(char *, char *, int);
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21
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22 int binSearch(char *);
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23
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24 int windowSearch(struct window *, int, int);
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25
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26 void saveDepth(char *);
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27
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28 #endif
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