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1 /*
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2 * This program is free software; you can redistribute it and/or modify
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3 * it under the terms of the GNU General Public License as published by
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4 * the Free Software Foundation; either version 3 of the License, or
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5 * (at your option) any later version.
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6 *
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7 * Written (W) 2010-2011 Jonas Behr, Regina Bohnert, Gunnar Raetsch
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8 * Copyright (C) 2010-2011 Max Planck Society
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9 */
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10
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11
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12 #ifndef __GET_READS_DIRECT_H__
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13 #define __GET_READS_DIRECT_H__
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14
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15 #include <vector>
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16 using std::vector;
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17 #include "read.h"
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18
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19 //static int g_flag_on = 0, g_flag_off = 0;
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20 static int left_flag_mask = strtol((char*) "0x40", 0, 0);
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21 static int right_flag_mask = strtol((char*) "0x80", 0, 0);
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22 static int reverse_flag_mask = strtol((char*) "0x10", 0, 0);
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23
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24 static int subsample = 1000;
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25 //static int collapse = 0;
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26
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27 int get_reads_from_bam(char* filename, char* region, vector<CRead*>* reads, char strand, int lsubsample);
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28
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29 #endif
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