Mercurial > repos > vipints > deseq_hts
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 |
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| date | Wed, 09 May 2012 20:43:47 -0400 |
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| -1:000000000000 | 0:94a108763d9e |
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| 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 |