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
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
|
/*
* Copyright (C) 2010 Regents of the University of Michigan
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
#include <stdio.h>
#include <stdlib.h>
#include <stdint.h>
#include "SmithWaterman.h"
// put TEST below here, so that makedepend will see the .h, so that we
// can get a clean dependency for SmithWaterman.o, so that we can at least
// compile the header when we change it.
#if defined(TEST)
#include <getopt.h>
#include "Generic.h"
// g++ -g -o testSW -DTEST SmithWaterman.cpp
//
// Smith-Waterman - test code uses a 256x256 array of int16
//
int swat(
bool showAllCases,
const char *A,
const char *qualities,
const char *B,
int direction,
const char *expectedCigarString,
int expectedSumQ
)
{
int allowedInsertDelete = 1024;
int errors = 0;
// read length 256
// reference length 1024
SmithWaterman<256, 1024, uint16_t, const char *, const char *, const char *, uint32_t, uint32_t > sw(&A, &qualities, &B, strlen(A), strlen(B), allowedInsertDelete, direction);
//
// now we align the read:
//
sw.populateH();
sw.populateAlignment();
int sumQ = sw.getSumQ();
CigarRoller cigar;
cigar.clear();
sw.rollCigar(cigar);
const char *cigarStr = cigar.getString();
//
// now we pretty print the results
//
bool badCigar = false, badQuality = false;
if (strcmp(cigarStr, expectedCigarString)!=0)
{
badCigar = true;
errors ++;
}
if (sumQ != expectedSumQ)
{
badQuality = true;
errors ++;
}
if (showAllCases || errors>0)
{
cout << "=============" << endl;
cout << " Read: " << A << endl;
cout << " Reference: " << B << endl;
cout << " Direction: " << direction << endl;
cout << "Max Cell: " << sw.maxCostValue << " located at " << sw.maxCostPosition << endl;
cout << "M: " << sw.m << " N: " << sw.n << endl;
cout << "Cigar String: " << cigarStr ;
if (badCigar)
cout << " (EXPECTED: " << expectedCigarString << ")";
cout << endl;
cout << " sumQ:" << sumQ;
if (badQuality)
cout << " (EXPECTED: " << expectedSumQ << ")";
cout << endl;
if (strlen(B) < 100 || showAllCases)
sw.printH(false);
for (vector<pair<int,int> >::iterator i = sw.alignment.begin(); i != sw.alignment.end(); i++) cout << *i << endl;
cout << "=============" << endl << endl;
}
delete cigarStr;
return errors;
}
// test with Sequence 1 = ACACACTA
// Sequence 2 = AGCACACA
int main(int argc, const char **argv)
{
int errors = 0;
bool showAllCasesFlag = false;
int opt;
while ((opt = getopt(argc, (char **) argv, "v")) != -1)
{
switch (opt)
{
case 'v':
showAllCasesFlag = true;
break;
default:
cerr << "usage: testSW [-v]" << std::endl;
exit(1);
}
}
// CIGAR explanation - for backward SW runs, the corresponding
// CIGAR string is generated from the back of the string to the
// front. Recall that the soft clipping is only done at the
// "end" of the string, taking direction into account.
// forwards - simple
errors += swat(showAllCasesFlag, "1234", "\"#$-", "1235", 1, "3M1S", 0);
// backwards - simple
errors += swat(showAllCasesFlag, "1234", "\"#$-", "1235", -1, "4M", 12);
// backwards - soft left clip
errors += swat(showAllCasesFlag, "1234", "\"#$-", "0234", -1, "1S3M", 0);
// delete in read (arg 1) - forward
errors += swat(showAllCasesFlag, "123467890", "\"#$%^&*()-", "1234567890", +1, "4M1D5M", 50);
// insert in read (arg 1) - forward
errors += swat(showAllCasesFlag, "1234556789", "\"#$%^&*()-", "1234567890", +1, "5M1I4M", 50);
// delete in read (arg 1) - backward
errors += swat(showAllCasesFlag, "X123467890", "#\"#$%^&*()-", "1234567890", -1, "1S4M1D5M", 50);
// insert in read (arg 1) - backward
errors += swat(showAllCasesFlag, "1234556789", "\"#$%^&*()-", "0123456789", -1, "4M1I5M", 50);
// insert in read (arg 1) - backward
errors += swat(showAllCasesFlag, "X1223456789", "00000000000", "00123456789", -1, "1S1M1I8M", 50);
// insert in read (arg 1) - backward
errors += swat(showAllCasesFlag, "XY1223456789", "000000000000", "000123456789", -1, "2S1M1I8M", 50);
// forward - soft right clip of 2 bases - sumQ should be 0
errors += swat(showAllCasesFlag, "123456700", "\"#$%^&*()-", "123456789", +1, "7M2S", 0);
// insert in read (arg 1) - forward w/2 mismatches at end
errors += swat(showAllCasesFlag, "1023456700", "\"#$%^&*()-", "123456789", +1, "1M1I6M2S", 50);
// insert in read (arg 1) - forward w/2 mismatches at end
errors += swat(showAllCasesFlag, "CTCCACCTCCCGGTT", "111111111111111", "TCCACCTCCCAGGTT", -1, "1S10M1D4M", 50);
//
errors += swat(showAllCasesFlag, "1234", "0000", "12345", +1, "4M", 0);
//
errors += swat(showAllCasesFlag, "1234X", "00000", "12345", +1, "4M1S", 0);
//
errors += swat(showAllCasesFlag, "4321", "0000", "7654321", -1, "4M", 0);
//
errors += swat(showAllCasesFlag, "X4321", "00000", "7654321", -1, "1S4M", 0);
//
errors += swat(showAllCasesFlag, "X432A10", "0000000", "76543210", -1, "1S3M1I2M", 50);
//
errors += swat(showAllCasesFlag, "1345", "0000", "12345", -1, "1M1D3M", 50);
errors += swat(showAllCasesFlag, "45689", "00000", "1234567890", -1, "3M1D2M", 50);
// errors += swat(showAllCasesFlag, "AATAATTTTTTATATACAGATCGCTGTAGAGTGTAGTTATAGTATGATTCCAACTTTTATTTCTTTCATGACTAATTATATGTATACATGTGCCATGTTGGTGTGCTG", "000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000", "TCCAATGTAGGGCTGTTATAAACAGTGTTGATACATATGTTTTTGTATAAGTCTTTGTTGAATACATGCTTTCATTTTTGTAGGGTATATGTCCAGGAATTAAATTTTTGCATTATTGGGGAAGTTCAAACGTAGATCAGTAGATGTTCCCAAATGATTTTCAGGATATGTATCCATGTAAATTCCTACCAGCAATGCAGGAGAATTCCAATTGCCCATGTTCTAATCAGAATATTGTTATATCCTAAGACTAATTTTAAATATTCTGATGGGTGTAGAGTGGAGGCATAGTATGATTTCAACTTGTATTTCTTTCATGACTAATTATCTTCTATGTTAATTGTTATTTTGTATGTTTATTGCAAAGTGCCTATCCAGAATTTTTGTCTATAATTTTGTTGTGCTGTCTCTTGCTTTATGAATTTTATAGGATTCTTAATATTATAATTGAGTTATCTTTCTTTTTTATTATTATTATTATACTTTAAGTTTTAGGGTATATGTGCACAACGTGCAAGTTTGTCACATATGTATACATGTGCCATGTTGGTGTGCTGCACCCATTAACTCATCATTTAGCATTAGGTATATCTCCTAATGCTATCCCTTCCTCCTCCCCCCACCCCACAACAGTCCCCGGTGTGTGATGTTCCCCTGCCTTTGTCCTCTTTCTTATACTTGCATGAGCAATCTCCTCAAACTGATACTTGCCTTTTTTGTCCTTGGTGTGGTTTGGCTCTGTGTTCCCACCCAAATCTTCATAATACCCATGTGCCAAGGGTGGGACTGGGTGGAGGTAATTGGGTCATGGGGATGGTTTCCCTCATACTATTATGATAGTGAGTGTTTTCACGAGACCTGATGGTTTTATAACTGTGTGGCATTTCCCTTGCTTCCACTCACTCCATCCTGCCACCCTGTGAAGAAGGTGCCTGCTTCTCCTTTGGTTACTGCTATGATTGTAAGTTTCCTGAGGCCTCCCCAGCAACGCAAAACTGTGAATCAATTAAACCTTTTTCCTTTATAAATTACTAAGTCTTGGGTATTTCTTCATAGTGTTGTGAGCATAGACTAAAACAGTAAGTTGTTACCAGGAGTGGGGTACTGCTGTAAGATAACTGAGAATGTGAAAGTGACTTAGGAACTAGGTAATGAGCAGAGGTTGGAACAGTTTAAAAGGCTCAGAAGAAGACAGAAAGATGTGGGAAAGTTTGGA", -1, "77M200D31M", 50);
errors += swat(showAllCasesFlag, "TTAGAATGCTATTGTGTTTGGAGATTTGAGGAAAGTGGGCGTGAAGACTTAGTGTTCATTTCCTCAACCTCTCTCTGTGTGAACATACGTCATCGGTCAGAAATTGGG", "000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000", "CCGAGATTGTGCCATTGCACTCCTGCCTGGGTAACAGAGTCAGACCCTGTCTCAAAAAAAAAAAAAAAAAAAAAAAAGATTAGGTTTTATAGATGGAAAATTCACAGCTCTCTCCAGATCAGAAATCTCCAAGAGTAAATTAGTGTCTTAAAGGGGTTGTAATAACTTTCCTATGTGACTAAGTGCATTATTAATCAATTTTTCTATGATCAAGTACTCCTTTACATACCTGCTAATACAATTTTTGATATGAAATCAGTCCTAGAGGGAATCAATGTAAGATACAGACTTGATGAGTGCTTGCAGTTTTTTATTGACAATCTGAAGAATGACTTGACTCTAAATTGCAGCTCAAGGCTTAGAATGCTATTGTGTTTGGAGATTTGAGGAAAGTGGGCGTGAAGACTTAGTGTTCATTTCCTCAACCTCTCTCTGTGTGAACATACAGGAATCAAATCTGTCTAGCCTCTCTTTTTGGCAAGGTTAAGAACAATTCCACTTCATCCTAATCCCAATGATTCCTGCCGACCCTCTTCCAAAAACTATTTAAAGACATGTTCTTCAAAGTTATATTTGTCTTTCCTTCAGGGAGAAAAAGAATACCAATCACTTATAATATGGAAACTAGCAGAAATGGGTCACATAAGTCATCTGTCAGAAATTGGGAAAATAGAGTAGGTCAGTCTTTCCAGTCATGGTACTTTTACCTTCAATCA", -1, "88M200D20M", 50);
// prefix TTAGAATGCTATTGTGTTTGGAGATTTGAGGAAAGTGGGCGTGAAGACTTAGTGTTCATTTCCTCAACCTCTCTCTGTGTGAACATAC
// suffix GTCATCTGTCAGAAATTGGGA
cout << endl << "Total Errors found: " << errors << endl;
}
#endif
|
