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root/gclib/tophat_cpp/insertions.cpp
Revision: 29
Committed: Tue Aug 2 21:24:54 2011 UTC (8 years, 9 months ago) by gpertea
File size: 4148 byte(s)
Log Message:
adding tophat source work

Line File contents
1 /*
2 * insertions.cpp
3 * TopHat
4 *
5 * Created by Ryan Kelley on 11/04/2010.
6 *
7 */
8
9 #ifdef HAVE_CONFIG_H
10 #include <config.h>
11 #else
12 #define PACKAGE_VERSION "INTERNAL"
13 #define SVN_REVISION "XXX"
14 #endif
15
16
17 #include <cassert>
18 #include <cstdio>
19 #include <cstring>
20 #include <vector>
21 #include <string>
22 #include <map>
23 #include <algorithm>
24 #include <set>
25 #include <stdexcept>
26 #include <iostream>
27 #include <fstream>
28 #include <seqan/sequence.h>
29 #include <seqan/find.h>
30 #include <seqan/file.h>
31 #include <getopt.h>
32
33 #include "common.h"
34 #include "bwt_map.h"
35 #include "junctions.h"
36 #include "insertions.h"
37 #include "fragments.h"
38 #include "wiggles.h"
39 #include "tokenize.h"
40 #include "reads.h"
41
42 #include "inserts.h"
43
44 /**
45 * Add insertions from an alignment to an InsertionSet.
46 * This will look for insertion in the alignment specified by bh. If the
47 * insertion is already in insertions, it will updated the count. Otherwise,
48 * it will add the insertion to the set and initialize the count to 1.
49 * @param bh The bowtie hit to be used to specify alignment infromation.
50 * @param insertions The InsertionSet that will be updated with the insertion information from teh alignment.
51 */
52 void insertions_from_alignment(const BowtieHit& bh, InsertionSet& insertions){
53
54 vector<Insertion> new_insertions;
55 insertions_from_spliced_hit(bh, new_insertions);
56
57 for(size_t i = 0; i < new_insertions.size(); ++i){
58 Insertion insertion = new_insertions[i];
59 InsertionSet::iterator itr = insertions.find(insertion);
60 if (itr != insertions.end()){
61 itr->second += 1;
62 }
63 else{
64 assert(insertion.refid != 0xFFFFFFFF);
65 insertions[insertion] = 1;
66 }
67 }
68 return;
69 }
70
71
72 /**
73 * Print insertions in BED format.
74 * Note, as per the BED-standard (http://genome.ucsc.edu/FAQ/FAQformat)
75 * -The coordinates should be 0-based
76 * -The chromEnd field should not include the actual feature
77 * -The name will be the inserted sequence
78 * -The score will be the number of supporing counts, which is capped at 1,000
79 * By (my) convention, the chromStart will be the last genome postion
80 * before hte insertio.
81 *
82 * <chrom>\t<left>\t<left>\t<inserted sequence>\t<read count>\n
83 * @param insertions_out The output file
84 * @param insertions Maps from insertions to number of supporting reads
85 * @param ref_sequences The table of reference sequences
86 */
87 void print_insertions(FILE* insertions_out, const InsertionSet& insertions, RefSequenceTable& ref_sequences){
88 fprintf(insertions_out, "track name=insertions description=\"TopHat insertions\"\n");
89 for(InsertionSet::const_iterator i = insertions.begin(); i != insertions.end(); ++i){
90 int counts = i->second;
91 if(counts > 1000){
92 counts = 1000;
93 }
94 fprintf(insertions_out, "%s\t%d\t%d\t%s\t%d\n",
95 ref_sequences.get_name(i->first.refid),
96 i->first.left,
97 i->first.left,
98 (i->first.sequence).c_str(),
99 counts);
100 }
101 }
102
103 /**
104 * Extract a list of insertions from a bowtie hit.
105 * Given a bowtie hit, extract a vector of insertions.
106 * @param bh The bowtie hit to use for alignment information.
107 * @param insertions Used to store the resultant vector of insertions.
108 */
109 void insertions_from_spliced_hit(const BowtieHit& bh, vector<Insertion>& insertions){
110 const vector<CigarOp>& cigar = bh.cigar();
111 unsigned int positionInGenome = bh.left();
112 unsigned int positionInRead = 0;
113
114 for(size_t c = 0; c < cigar.size(); ++c){
115 Insertion insertion;
116 switch(cigar[c].opcode){
117 case REF_SKIP:
118 positionInGenome += cigar[c].length;
119 break;
120 case MATCH:
121 positionInGenome += cigar[c].length;
122 positionInRead += cigar[c].length;
123 break;
124 case DEL:
125 positionInGenome += cigar[c].length;
126 break;
127 case INS:
128 /*
129 * Note that the reported position in the genome from the SAM
130 * alignment is 1-based, since the insertion object is expecting
131 * a 0-based co-ordinate, we need to subtract 1
132 */
133 insertion.refid = bh.ref_id();
134 insertion.left = positionInGenome-1;
135 insertion.sequence = bh.seq().substr(positionInRead, cigar[c].length);
136
137 insertions.push_back(insertion);
138 positionInRead += cigar[c].length;
139 break;
140 default:
141 break;
142 }
143 }
144 return;
145 }