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annotate rDiff/src/tools/read_utils/get_reads_direct.h @ 2:233c30f91d66

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updated python based GFF parsing module which will handle GTF/GFF/GFF3 file types
author vipints <vipin@cbio.mskcc.org>
date Tue, 08 Oct 2013 07:15:44 -0400
parents 0f80a5141704
children
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1 /* written by Jonas Behr, Regina Bohnert and Gunnar Raetsch, FML Tuebingen, Germany, 2010 */
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2
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3 #ifndef __GET_READS_DIRECT_H__
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4 #define __GET_READS_DIRECT_H__
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5
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6 #include <vector>
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7 using std::vector;
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8 #include "read.h"
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9 #include <stdlib.h>
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10 #include "sam.h"
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11
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12 //static int g_flag_on = 0, g_flag_off = 0;
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13 static int left_flag_mask = strtol((char*) "0x40", 0, 0);
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14 static int right_flag_mask = strtol((char*) "0x80", 0, 0);
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15 static int reverse_flag_mask = strtol((char*) "0x10", 0, 0);
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16
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17 static int subsample = 1000;
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18 //static int collapse = 0;
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19
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20 int get_reads_from_bam(char* filename, char* region, vector<CRead*>* reads, char strand, int lsubsample);
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21 void parse_cigar(bam1_t* b, CRead* read, bam_header_t* header);
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22
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23 #endif