-
Notifications
You must be signed in to change notification settings - Fork 2
/
t_capmq.c
177 lines (139 loc) · 6.54 KB
/
t_capmq.c
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
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
/* The MIT License
Copyright (C) 2017 Genome Research Ltd.
Author: Jennifer Liddle <js10@sanger.ac.uk>
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in
all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE. */
#include <stdio.h>
#include <stdbool.h>
#include <stdlib.h>
#include <string.h>
bool verbose = true;
typedef int (*content_test_func)(FILE *f, char *expected);
int sam_content_test(FILE *f, char *expected) {
char res_str[1024];
size_t n;
int nPG=0;
int om[6]={0,0,0,0,0,0};
int q[6];
int nlines = 0;
char *lineptr = NULL;
while (getline(&lineptr, &n, f) != -1) {
if (strncmp(lineptr,"@PG",3) == 0) nPG++;;
if (*lineptr != '@') { // read line, not header line
char *s;
char *col;
int colnum;
if (nlines < 6) {
col = strtok(lineptr, "\t");
for (colnum=0; colnum < 4; colnum++) {
col = strtok(NULL, "\t");
}
q[nlines] = col!=NULL ? atoi(col) : -1;
for (colnum=0; colnum < 7; colnum++) {
strtok(NULL, "\t");
}
while ((col = strtok(NULL, "\t")) != NULL) {
s = strstr(col, "om:i:");
om[nlines] = s!=NULL ? atoi(s+5) : -1;
}
}
nlines++;
}
}
free(lineptr);
sprintf(res_str,"%d %d om[%d,%d,%d,%d,%d,%d] q[%d,%d,%d,%d,%d,%d]",
nlines, nPG, om[0], om[1], om[2], om[3], om[4], om[5], q[0], q[1], q[2], q[3], q[4], q[5]);
if (strcmp(res_str,expected)) {
fprintf(stderr,"Expected: %s\n",expected);
fprintf(stderr,"Actual: %s\n",res_str);
return 1;
}
return 0;
}
int content_contains_test(FILE *f, char *expected) {
size_t n;
int nlines = 0;
char *lineptr = NULL;
while (getline(&lineptr, &n, f) != -1) {
nlines++;
char *s;
s = strstr(lineptr, expected);
if (s != NULL) {
return 0;
}
}
free(lineptr);
fprintf(stderr, "Expected string not found in any output line: %s\n", expected);
return 1;
}
int run_test(char *cmd, char *expected, int expected_status, content_test_func test)
{
if (verbose) fprintf(stderr, "Testing command: %s\n", cmd);
FILE *f = popen(cmd, "r");
if (!f) {
fprintf(stderr,"Can't run command: %s\n", cmd);
return 1;
}
int result = test(f, expected);
int status = pclose(f);
if (WIFEXITED(status)) {
int exit_status = WEXITSTATUS(status);
if (exit_status != expected_status) {
fprintf(stderr, "Expected exit status: %d\n", expected_status);
fprintf(stderr, "Actual exit status: %d\n", exit_status);
return 1;
}
} else {
fprintf(stderr, "Program did not exit normally\n");
return 1;
}
return result;
}
int main(int argc, char *argv[])
{
int pass=0, fail=0;
// this should do nothing except add @PG, because no MQ is over 100
if (run_test("./capmq -C100 test1.sam","6 1 om[-1,-1,-1,-1,-1,-1] q[45,46,47,48,4,4]",0,&sam_content_test)) fail++; else pass++;
// cap all values, and create om tags
if (run_test("./capmq -C40 test1.sam","6 1 om[45,46,47,48,-1,-1] q[40,40,40,40,4,4]",0,&sam_content_test)) fail++; else pass++;
// this should cap all mapping qualities at 0
if (run_test("./capmq -C0 test1.sam","6 1 om[45,46,47,48,4,4] q[0,0,0,0,0,0]",0,&sam_content_test)) fail++; else pass++;
// cap and restore. End result should be unchanged
if (run_test("./capmq -C40 test1.sam | ./capmq -r","6 2 om[-1,-1,-1,-1,-1,-1] q[45,46,47,48,4,4]",0,&sam_content_test)) fail++; else pass++;
// cap and cap and restore. End result should still be unchanged
if (run_test("./capmq -C41 test1.sam | ./capmq -C 5 | ./capmq -r","6 3 om[-1,-1,-1,-1,-1,-1] q[45,46,47,48,4,4]",0,&sam_content_test)) fail++; else pass++;
// read groups, no default cap
if (run_test("./capmq -gb:41 -ga:40 -gx:42 test1.sam","6 1 om[45,46,47,48,-1,-1] q[40,40,41,41,4,4]",0,&sam_content_test)) fail++; else pass++;
// read groups, with default cap
if (run_test("./capmq -C40 -ga:41 test1.sam","6 1 om[45,46,47,48,-1,-1] q[41,41,40,40,4,4]",0,&sam_content_test)) fail++; else pass++;
// cap value using freemix
if (run_test("./capmq -S -C0.00005 -f test1.sam","6 1 om[-1,-1,-1,-1,-1,-1] q[43,43,43,43,4,4]",0,&sam_content_test)) fail++; else pass++;
// read groups using freemix
if (run_test("./capmq -S -gb:0.00005 -f -ga:0.0001 test1.sam","6 1 om[-1,-1,-1,-1,-1,-1] q[40,40,43,43,4,4]",0,&sam_content_test)) fail++; else pass++;
// read groups using freemix and -m
if (run_test("./capmq -m41 -S -gb:0.00005 -f -ga:0.0001 test1.sam","6 1 om[-1,-1,-1,-1,-1,-1] q[41,41,43,43,4,4]",0,&sam_content_test)) fail++; else pass++;
// read groups from file
if (run_test("./capmq -S -f -G test-b-a.txt test1.sam","6 1 om[-1,-1,-1,-1,-1,-1] q[40,40,43,43,4,4]",0,&sam_content_test)) fail++; else pass++;
// read groups from file - override `a' with minimum
if (run_test("./capmq -m41 -S -f -G test-b-a.txt test1.sam","6 1 om[-1,-1,-1,-1,-1,-1] q[41,41,43,43,4,4]",0,&sam_content_test)) fail++; else pass++;
// read groups from file - RG `a' not matched
if (run_test("./capmq -m41 -S -f -G test-b-ai.txt test1.sam","6 1 om[-1,-1,-1,-1,-1,-1] q[45,46,43,43,4,4]",0,&sam_content_test)) fail++; else pass++;
// this should do nothing and say so
if (run_test("./capmq test1.sam 2>&1","Nothing to do",1,&content_contains_test)) fail++; else pass++;
printf("Passed %d tests\n", pass);
if (fail) printf("FAILED %d tests\n", fail);
return fail;
}