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1 /*
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2 * Copyright (c) <2008 - 2009>, University of Washington, Simon Fraser University
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3 * All rights reserved.
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4 *
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5 * Redistribution and use in source and binary forms, with or without modification,
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6 * are permitted provided that the following conditions are met:
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7 *
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8 * Redistributions of source code must retain the above copyright notice, this list
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9 * of conditions and the following disclaimer.
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10 * - Redistributions in binary form must reproduce the above copyright notice, this
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11 * list of conditions and the following disclaimer in the documentation and/or other
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12 * materials provided with the distribution.
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13 * - Neither the name of the <ORGANIZATION> nor the names of its contributors may be
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14 * used to endorse or promote products derived from this software without specific
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15 * prior written permission.
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16 *
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17 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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18 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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19 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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20 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR
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21 * CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
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22 * EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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23 * PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR
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24 * PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF
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25 * LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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26 * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
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27 * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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28 */
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29
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30 /*
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31 * Author : Faraz Hach
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32 * Email : fhach AT cs DOT sfu
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33 * Last Update : 2009-12-08
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34 */
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35
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36
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37 #ifndef __OUTPUT__
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38 #define __OUTPUT__
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39
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40 #define FORWARD 0
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41 #define REVERSE 1
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42
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43 typedef struct
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44 {
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45 char *tag;
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46 char type;
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47 char cVal;
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48 int iVal;
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49 float fVal;
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50 char *sVal;
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51 } OPT_FIELDS;
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52
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53 typedef struct
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54 {
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55 char *QNAME;
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56 short FLAG;
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57 char *RNAME;
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58 int POS;
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59 unsigned char MAPQ;
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60 char *CIGAR;
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61 char *MRNAME;
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62 int MPOS;
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63 int ISIZE;
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64 char *SEQ;
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65 char *QUAL;
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66
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67 int optSize;
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68 OPT_FIELDS *optFields;
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69 } SAM;
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70
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71 int initOutput(char *fileName, int compressed);
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72 void (*finalizeOutput)();
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73 void (*output)(SAM map);
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74
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75
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76 #endif
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