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comparison rDiff/src/tools/read_utils/get_reads_direct.h @ 0:0f80a5141704

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version 0.3 uploaded
author vipints
date Thu, 14 Feb 2013 23:38:36 -0500
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-1:000000000000 0:0f80a5141704
1 /* written by Jonas Behr, Regina Bohnert and Gunnar Raetsch, FML Tuebingen, Germany, 2010 */
2
3 #ifndef __GET_READS_DIRECT_H__
4 #define __GET_READS_DIRECT_H__
5
6 #include <vector>
7 using std::vector;
8 #include "read.h"
9 #include <stdlib.h>
10 #include "sam.h"
11
12 //static int g_flag_on = 0, g_flag_off = 0;
13 static int left_flag_mask = strtol((char*) "0x40", 0, 0);
14 static int right_flag_mask = strtol((char*) "0x80", 0, 0);
15 static int reverse_flag_mask = strtol((char*) "0x10", 0, 0);
16
17 static int subsample = 1000;
18 //static int collapse = 0;
19
20 int get_reads_from_bam(char* filename, char* region, vector<CRead*>* reads, char strand, int lsubsample);
21 void parse_cigar(bam1_t* b, CRead* read, bam_header_t* header);
22
23 #endif