comparison deseq-hts_1.0/mex/get_reads_direct.h @ 0:94a108763d9e draft

deseq-hts version 1.0 wraps the DESeq 1.6.0
author vipints
date Wed, 09 May 2012 20:43:47 -0400
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-1:000000000000 0:94a108763d9e
1 /*
2 * This program is free software; you can redistribute it and/or modify
3 * it under the terms of the GNU General Public License as published by
4 * the Free Software Foundation; either version 3 of the License, or
5 * (at your option) any later version.
6 *
7 * Written (W) 2010-2011 Jonas Behr, Regina Bohnert, Gunnar Raetsch
8 * Copyright (C) 2010-2011 Max Planck Society
9 */
10
11
12 #ifndef __GET_READS_DIRECT_H__
13 #define __GET_READS_DIRECT_H__
14
15 #include <vector>
16 using std::vector;
17 #include "read.h"
18
19 //static int g_flag_on = 0, g_flag_off = 0;
20 static int left_flag_mask = strtol((char*) "0x40", 0, 0);
21 static int right_flag_mask = strtol((char*) "0x80", 0, 0);
22 static int reverse_flag_mask = strtol((char*) "0x10", 0, 0);
23
24 static int subsample = 1000;
25 //static int collapse = 0;
26
27 int get_reads_from_bam(char* filename, char* region, vector<CRead*>* reads, char strand, int lsubsample);
28
29 #endif