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

deseq-hts version 1.0 wraps the DESeq 1.6.0

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/deseq-hts_1.0/mex/get_reads_direct.h	Wed May 09 20:43:47 2012 -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