1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
|
/* Philip T.L.C. Clausen Sep 2021 plan@dtu.dk */
/*
* Copyright (c) 2021, Philip Clausen, Technical University of Denmark
* All rights reserved.
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
#include <stdio.h>
#include <math.h>
#include "assembly.h"
#include "tsv.h"
#define printsvField(flag, outfile, format, feature) if(flag & 1) {fprintf(outfile, format, feature, (flag >>= 1) ? '\t' : '\n');} else {flag >>= 1;}
void initsv(FILE *outfile, long unsigned flag) {
/* mask off invalid flags */
flag &= 65535;
printsvField(flag, outfile, "%s%c", "Template_Name");
printsvField(flag, outfile, "%s%c", "Template_Length");
printsvField(flag, outfile, "%s%c", "Template_Identity");
printsvField(flag, outfile, "%s%c", "Template_Coverage");
printsvField(flag, outfile, "%s%c", "Template_Depth");
printsvField(flag, outfile, "%s%c", "Query_Identity");
printsvField(flag, outfile, "%s%c", "Query_Coverage");
printsvField(flag, outfile, "%s%c", "Query_Depth");
printsvField(flag, outfile, "%s%c", "Read_Count_Map");
printsvField(flag, outfile, "%s%c", "Read_Count_Aln");
printsvField(flag, outfile, "%s%c", "Score");
printsvField(flag, outfile, "%s%c", "Expected");
printsvField(flag, outfile, "%s%c", "q_value");
printsvField(flag, outfile, "%s%c", "p_value");
printsvField(flag, outfile, "%s%c", "ConClave_Score");
printsvField(flag, outfile, "%s%c", "ConClave_Quality");
}
void printsv(FILE *outfile, long unsigned flag, char *template_name, Assem *aligned_assem, int t_len, unsigned readCount, long unsigned read_score, double expected, double q_value, double p_value, long unsigned ConClave_Score) {
//printsv(tsv_out, tsv, template_name, aligned_assem, t_len, readCount, read_score, expected, q_value, p_value, alignment_scores[template]);
/* mask off invalid flags */
flag &= 65535;
/* 0 no file */
if(!flag) {
return;
}
/* 1 Template_Name */
printsvField(flag, outfile, "%s%c", template_name);
/* 2 Template_Length */
printsvField(flag, outfile, "%d%c", t_len);
/* 4 Template_Identity */
printsvField(flag, outfile, "%f%c", 100.0 * aligned_assem->cover / t_len);
/* 8 Template_Coverage */
printsvField(flag, outfile, "%f%c", 100.0 * aligned_assem->aln_len / t_len);
/* 16 Template_Depth */
printsvField(flag, outfile, "%f%c", (double)(aligned_assem->depth) / t_len);
/* 32 Query_Identity */
printsvField(flag, outfile, "%f%c", 100.0 * aligned_assem->cover / aligned_assem->aln_len);
/* 64 Query_Coverage */
printsvField(flag, outfile, "%f%c", 100.0 * aligned_assem->cover / aligned_assem->aln_len);
/* 128 Query_Depth */
printsvField(flag, outfile, "%f%c", (double)(aligned_assem->depth) / aligned_assem->aln_len);
/* 256 Read_Count_Map */
printsvField(flag, outfile, "%d%c", readCount);
/* 512 Read_Count_Aln */
printsvField(flag, outfile, "%d%c", aligned_assem->readCountAln);
/* 1024 Score */
printsvField(flag, outfile, "%lu%c", read_score);
/* 2048 Expected */
printsvField(flag, outfile, "%f%c", expected);
/* 4096 q_value */
printsvField(flag, outfile, "%f%c", q_value);
/* 8192 p_value */
printsvField(flag, outfile, "%e%c", p_value);
/* 16384 ConClave_Score */
printsvField(flag, outfile, "%lu%c", ConClave_Score);
/* 32768 ConClave_Quality */
printsvField(flag, outfile, "%f%c", 40.0 * read_score / ConClave_Score * log(read_score));
}
|
