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root/gclib/tophat_cpp/deletions.h
Revision: 154
Committed: Tue Jan 24 02:29:21 2012 UTC (7 years, 9 months ago) by gpertea
File size: 834 byte(s)
Log Message:
massive update with Daehwan's work

Line File contents
1 #ifndef DELETIONS_H
2 #define DELETIONS_H
3 /*
4 * deletions.h
5 * TopHat
6 *
7 * Created by Ryan Kelley on 11/09/2010
8 *
9 */
10
11 #include <cstdio>
12 #include <vector>
13 #include <string>
14 #include <set>
15 #include <iostream>
16 #include <fstream>
17 #include <cstring>
18 #include <seqan/sequence.h>
19 #include <seqan/find.h>
20 #include <seqan/file.h>
21
22 #include "bwt_map.h"
23 #include "junctions.h"
24 using namespace std;
25
26
27 typedef Junction Deletion;
28 typedef std::map<Junction, uint32_t> DeletionSet;
29
30 void deletions_from_alignment(const BowtieHit& spliced_alignment, DeletionSet& junctions);
31
32 void deletions_from_spliced_hit(const BowtieHit& bh, vector<Deletion>& deletions);
33
34 void print_deletions(FILE* deletions_out, const DeletionSet& deletions, RefSequenceTable& ref_sequences);
35
36 void merge_with(DeletionSet& deletions, const DeletionSet& other);
37
38 #endif