Mercurial > repos > vipints > deseq_hts
diff deseq-hts_2.0/mex/get_reads_direct.h @ 10:2fe512c7bfdf draft
DESeq2 version 1.0.19 added to the repo
| author | vipints <vipin@cbio.mskcc.org> |
|---|---|
| date | Tue, 08 Oct 2013 08:15:34 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/deseq-hts_2.0/mex/get_reads_direct.h Tue Oct 08 08:15:34 2013 -0400 @@ -0,0 +1,29 @@ +/* +* This program is free software; you can redistribute it and/or modify +* it under the terms of the GNU General Public License as published by +* the Free Software Foundation; either version 3 of the License, or +* (at your option) any later version. +* +* Written (W) 2010-2011 Jonas Behr, Regina Bohnert, Gunnar Raetsch +* Copyright (C) 2010-2011 Max Planck Society +*/ + + +#ifndef __GET_READS_DIRECT_H__ +#define __GET_READS_DIRECT_H__ + +#include <vector> + using std::vector; +#include "read.h" + +//static int g_flag_on = 0, g_flag_off = 0; +static int left_flag_mask = strtol((char*) "0x40", 0, 0); +static int right_flag_mask = strtol((char*) "0x80", 0, 0); +static int reverse_flag_mask = strtol((char*) "0x10", 0, 0); + +static int subsample = 1000; +//static int collapse = 0; + +int get_reads_from_bam(char* filename, char* region, vector<CRead*>* reads, char strand, int lsubsample); + +#endif