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TestCigarHelper.cpp
1/*
2 * Copyright (C) 2011 Regents of the University of Michigan
3 *
4 * This program is free software: you can redistribute it and/or modify
5 * it under the terms of the GNU General Public License as published by
6 * the Free Software Foundation, either version 3 of the License, or
7 * (at your option) any later version.
8 *
9 * This program is distributed in the hope that it will be useful,
10 * but WITHOUT ANY WARRANTY; without even the implied warranty of
11 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
12 * GNU General Public License for more details.
13 *
14 * You should have received a copy of the GNU General Public License
15 * along with this program. If not, see <http://www.gnu.org/licenses/>.
16 */
17
18#include "TestCigarHelper.h"
19#include "TestValidate.h"
20#include "CigarHelper.h"
21#include <assert.h>
22
23void testCigarHelper()
24{
25 // Call generic test.
26 CigarHelperTest::testCigarHelper();
27}
28
29
30void CigarHelperTest::testCigarHelper()
31{
32 testSoftClipBeginByRefPos();
33 testSoftClipEndByRefPos();
34}
35
36
37void CigarHelperTest::testSoftClipBeginByRefPos()
38{
39 SamRecord record;
40 CigarRoller newCigar;
41 std::string newCigarString;
42 int32_t newPos = 0;
43
44 // Setup the current Cigar.
45 // Cigar: HHHSSSMMMDDDMMMIIIMMMPPPMMMDDDMMMSSSHHH
46 // ReadPos: 000000 000011111 111 112222
47 // ReadPos: 012345 678901234 567 890123
48 // RefPos: 111111111 122 222222223
49 // RefPos: 012345678 901 234567890
50 const char* origCigar = "3H3S3M3D3M3I3M3P3M3D3M3S3H";
51 record.setCigar(origCigar);
52 record.set0BasedPosition(10);
53 record.setSequence("gggAAATTTCCCTTTGGGAAAggg");
54
55 ////////////////////////////////////////////////////////
56 // Clip outside of the range (after). Everything should be clipped.
57 assert(CigarHelper::softClipBeginByRefPos(record, 10000, newCigar, newPos) == 23);
58 newCigar.getCigarString(newCigarString);
59 assert(strcmp(newCigarString.c_str(), "3H24S3H") == 0);
60
61 ////////////////////////////////////////////////////////
62 // Clip outside of the range (before). Nothing should change.
63 assert(CigarHelper::softClipBeginByRefPos(record, 1, newCigar, newPos) ==
64 CigarHelper::NO_CLIP);
65 newCigar.getCigarString(newCigarString);
66 assert(strcmp(newCigarString.c_str(), origCigar) == 0);
67
68
69 ////////////////////////////////////////////////////////
70 ////////////////////////////////////////////////////////
71 // Test clipping at every position of the read.
72
73 ////////////////////////////////////////////////////////
74 // Clip at the first position.
75 assert(CigarHelper::softClipBeginByRefPos(record, 10, newCigar, newPos) == 3);
76 assert(newPos == 11);
77 newCigar.getCigarString(newCigarString);
78 //std::cout << newCigarString.c_str() << std::endl;
79 assert(strcmp(newCigarString.c_str(), "3H4S2M3D3M3I3M3P3M3D3M3S3H") == 0);
80
81 ////////////////////////////////////////////////////////
82 // Clip in the middle of the first Match.
83 assert(CigarHelper::softClipBeginByRefPos(record, 11, newCigar, newPos) == 4);
84 assert(newPos == 12);
85 newCigar.getCigarString(newCigarString);
86 //std::cout << newCigarString.c_str() << std::endl;
87 assert(strcmp(newCigarString.c_str(), "3H5S1M3D3M3I3M3P3M3D3M3S3H") == 0);
88
89 ////////////////////////////////////////////////////////
90 assert(CigarHelper::softClipBeginByRefPos(record, 12, newCigar, newPos) == 5);
91 assert(newPos == 16);
92 newCigar.getCigarString(newCigarString);
93 //std::cout << newCigarString.c_str() << std::endl;
94 assert(strcmp(newCigarString.c_str(), "3H6S3M3I3M3P3M3D3M3S3H") == 0);
95
96 ////////////////////////////////////////////////////////
97 assert(CigarHelper::softClipBeginByRefPos(record, 13, newCigar, newPos) == 5);
98 assert(newPos == 16);
99 newCigar.getCigarString(newCigarString);
100 //std::cout << newCigarString.c_str() << std::endl;
101 assert(strcmp(newCigarString.c_str(), "3H6S3M3I3M3P3M3D3M3S3H") == 0);
102
103 ////////////////////////////////////////////////////////
104 assert(CigarHelper::softClipBeginByRefPos(record, 14, newCigar, newPos) == 5);
105 assert(newPos == 16);
106 newCigar.getCigarString(newCigarString);
107 //std::cout << newCigarString.c_str() << std::endl;
108 assert(strcmp(newCigarString.c_str(), "3H6S3M3I3M3P3M3D3M3S3H") == 0);
109
110 ////////////////////////////////////////////////////////
111 assert(CigarHelper::softClipBeginByRefPos(record, 15, newCigar, newPos) == 5);
112 assert(newPos == 16);
113 newCigar.getCigarString(newCigarString);
114 //std::cout << newCigarString.c_str() << std::endl;
115 assert(strcmp(newCigarString.c_str(), "3H6S3M3I3M3P3M3D3M3S3H") == 0);
116
117 ////////////////////////////////////////////////////////
118 assert(CigarHelper::softClipBeginByRefPos(record, 16, newCigar, newPos) == 6);
119 assert(newPos == 17);
120 newCigar.getCigarString(newCigarString);
121 //std::cout << newCigarString.c_str() << std::endl;
122 assert(strcmp(newCigarString.c_str(), "3H7S2M3I3M3P3M3D3M3S3H") == 0);
123
124 ////////////////////////////////////////////////////////
125 assert(CigarHelper::softClipBeginByRefPos(record, 17, newCigar, newPos) == 7);
126 assert(newPos == 18);
127 newCigar.getCigarString(newCigarString);
128 //std::cout << newCigarString.c_str() << std::endl;
129 assert(strcmp(newCigarString.c_str(), "3H8S1M3I3M3P3M3D3M3S3H") == 0);
130
131 ////////////////////////////////////////////////////////
132 assert(CigarHelper::softClipBeginByRefPos(record, 18, newCigar, newPos) == 11);
133 assert(newPos == 19);
134 newCigar.getCigarString(newCigarString);
135 //std::cout << newCigarString.c_str() << std::endl;
136 assert(strcmp(newCigarString.c_str(), "3H12S3M3P3M3D3M3S3H") == 0);
137
138 ////////////////////////////////////////////////////////
139 assert(CigarHelper::softClipBeginByRefPos(record, 19, newCigar, newPos) == 12);
140 assert(newPos == 20);
141 newCigar.getCigarString(newCigarString);
142 //std::cout << newCigarString.c_str() << std::endl;
143 assert(strcmp(newCigarString.c_str(), "3H13S2M3P3M3D3M3S3H") == 0);
144
145 ////////////////////////////////////////////////////////
146 assert(CigarHelper::softClipBeginByRefPos(record, 20, newCigar, newPos) == 13);
147 assert(newPos == 21);
148 newCigar.getCigarString(newCigarString);
149 //std::cout << newCigarString.c_str() << std::endl;
150 assert(strcmp(newCigarString.c_str(), "3H14S1M3P3M3D3M3S3H") == 0);
151
152 ////////////////////////////////////////////////////////
153 assert(CigarHelper::softClipBeginByRefPos(record, 21, newCigar, newPos) == 14);
154 assert(newPos == 22);
155 newCigar.getCigarString(newCigarString);
156 //std::cout << newCigarString.c_str() << std::endl;
157 assert(strcmp(newCigarString.c_str(), "3H15S3M3D3M3S3H") == 0);
158
159 ////////////////////////////////////////////////////////
160 assert(CigarHelper::softClipBeginByRefPos(record, 22, newCigar, newPos) == 15);
161 assert(newPos == 23);
162 newCigar.getCigarString(newCigarString);
163 //std::cout << newCigarString.c_str() << std::endl;
164 assert(strcmp(newCigarString.c_str(), "3H16S2M3D3M3S3H") == 0);
165
166 ////////////////////////////////////////////////////////
167 assert(CigarHelper::softClipBeginByRefPos(record, 23, newCigar, newPos) == 16);
168 assert(newPos == 24);
169 newCigar.getCigarString(newCigarString);
170 //std::cout << newCigarString.c_str() << std::endl;
171 assert(strcmp(newCigarString.c_str(), "3H17S1M3D3M3S3H") == 0);
172
173 ////////////////////////////////////////////////////////
174 assert(CigarHelper::softClipBeginByRefPos(record, 24, newCigar, newPos) == 17);
175 assert(newPos == 28);
176 newCigar.getCigarString(newCigarString);
177 //std::cout << newCigarString.c_str() << std::endl;
178 assert(strcmp(newCigarString.c_str(), "3H18S3M3S3H") == 0);
179
180 ////////////////////////////////////////////////////////
181 assert(CigarHelper::softClipBeginByRefPos(record, 25, newCigar, newPos) == 17);
182 assert(newPos == 28);
183 newCigar.getCigarString(newCigarString);
184 //std::cout << newCigarString.c_str() << std::endl;
185 assert(strcmp(newCigarString.c_str(), "3H18S3M3S3H") == 0);
186
187 ////////////////////////////////////////////////////////
188 assert(CigarHelper::softClipBeginByRefPos(record, 26, newCigar, newPos) == 17);
189 assert(newPos == 28);
190 newCigar.getCigarString(newCigarString);
191 //std::cout << newCigarString.c_str() << std::endl;
192 assert(strcmp(newCigarString.c_str(), "3H18S3M3S3H") == 0);
193
194 ////////////////////////////////////////////////////////
195 assert(CigarHelper::softClipBeginByRefPos(record, 27, newCigar, newPos) == 17);
196 assert(newPos == 28);
197 newCigar.getCigarString(newCigarString);
198 //std::cout << newCigarString.c_str() << std::endl;
199 assert(strcmp(newCigarString.c_str(), "3H18S3M3S3H") == 0);
200
201 ////////////////////////////////////////////////////////
202 assert(CigarHelper::softClipBeginByRefPos(record, 28, newCigar, newPos) == 18);
203 assert(newPos == 29);
204 newCigar.getCigarString(newCigarString);
205 //std::cout << newCigarString.c_str() << std::endl;
206 assert(strcmp(newCigarString.c_str(), "3H19S2M3S3H") == 0);
207
208 ////////////////////////////////////////////////////////
209 assert(CigarHelper::softClipBeginByRefPos(record, 29, newCigar, newPos) == 19);
210 assert(newPos == 30);
211 newCigar.getCigarString(newCigarString);
212 //std::cout << newCigarString.c_str() << std::endl;
213 assert(strcmp(newCigarString.c_str(), "3H20S1M3S3H") == 0);
214
215 ////////////////////////////////////////////////////////
216 assert(CigarHelper::softClipBeginByRefPos(record, 30, newCigar, newPos) == 23);
217 assert(newPos == 10);
218 newCigar.getCigarString(newCigarString);
219 //std::cout << newCigarString.c_str() << std::endl;
220 assert(strcmp(newCigarString.c_str(), "3H24S3H") == 0);
221
222 ////////////////////////////////////////////////////////
223 assert(CigarHelper::softClipBeginByRefPos(record, 31, newCigar, newPos) == 23);
224 assert(newPos == 10);
225 newCigar.getCigarString(newCigarString);
226 //std::cout << newCigarString.c_str() << std::endl;
227 assert(strcmp(newCigarString.c_str(), "3H24S3H") == 0);
228
229 ////////////////////////////////////////////////////////
230 ////////////////////////////////////////////////////////
231 // Test clipping at every position when insertions & deletions
232 // are next to each other.
233 origCigar = "3M3D3I3M";
234 record.setCigar(origCigar);
235 record.setSequence("GGGAAAGGG");
236 // Cigar: MMMDDDIIIMMM
237 // ReadPos: 000 000000
238 // ReadPos: 012 345678
239 // RefPos: 111111 111
240 // RefPos: 012345 678
241 record.setCigar(origCigar);
242 assert(CigarHelper::softClipBeginByRefPos(record, 9, newCigar, newPos) ==
243 CigarHelper::NO_CLIP);
244 assert(newPos == 10);
245 newCigar.getCigarString(newCigarString);
246 //std::cout << newCigarString.c_str() << std::endl;
247 assert(strcmp(newCigarString.c_str(), origCigar) == 0);
248
249 record.setCigar(origCigar);
250 assert(CigarHelper::softClipBeginByRefPos(record, 10, newCigar, newPos) == 0);
251 assert(newPos == 11);
252 newCigar.getCigarString(newCigarString);
253 //std::cout << newCigarString.c_str() << std::endl;
254 assert(strcmp(newCigarString.c_str(), "1S2M3D3I3M") == 0);
255
256 record.setCigar(origCigar);
257 assert(CigarHelper::softClipBeginByRefPos(record, 11, newCigar, newPos) == 1);
258 assert(newPos == 12);
259 newCigar.getCigarString(newCigarString);
260 //std::cout << newCigarString.c_str() << std::endl;
261 assert(strcmp(newCigarString.c_str(), "2S1M3D3I3M") == 0);
262
263 record.setCigar(origCigar);
264 assert(CigarHelper::softClipBeginByRefPos(record, 12, newCigar, newPos) == 5);
265 assert(newPos == 16);
266 newCigar.getCigarString(newCigarString);
267 //std::cout << newCigarString.c_str() << std::endl;
268 assert(strcmp(newCigarString.c_str(), "6S3M") == 0);
269
270 record.setCigar(origCigar);
271 assert(CigarHelper::softClipBeginByRefPos(record, 13, newCigar, newPos) == 5);
272 assert(newPos == 16);
273 newCigar.getCigarString(newCigarString);
274 //std::cout << newCigarString.c_str() << std::endl;
275 assert(strcmp(newCigarString.c_str(), "6S3M") == 0);
276
277 record.setCigar(origCigar);
278 assert(CigarHelper::softClipBeginByRefPos(record, 14, newCigar, newPos) == 5);
279 assert(newPos == 16);
280 newCigar.getCigarString(newCigarString);
281 //std::cout << newCigarString.c_str() << std::endl;
282 assert(strcmp(newCigarString.c_str(), "6S3M") == 0);
283
284 record.setCigar(origCigar);
285 assert(CigarHelper::softClipBeginByRefPos(record, 15, newCigar, newPos) == 5);
286 assert(newPos == 16);
287 newCigar.getCigarString(newCigarString);
288 //std::cout << newCigarString.c_str() << std::endl;
289 assert(strcmp(newCigarString.c_str(), "6S3M") == 0);
290
291 record.setCigar(origCigar);
292 assert(CigarHelper::softClipBeginByRefPos(record, 16, newCigar, newPos) == 6);
293 assert(newPos == 17);
294 newCigar.getCigarString(newCigarString);
295 //std::cout << newCigarString.c_str() << std::endl;
296 assert(strcmp(newCigarString.c_str(), "7S2M") == 0);
297
298 record.setCigar(origCigar);
299 assert(CigarHelper::softClipBeginByRefPos(record, 17, newCigar, newPos) == 7);
300 assert(newPos == 18);
301 newCigar.getCigarString(newCigarString);
302 //std::cout << newCigarString.c_str() << std::endl;
303 assert(strcmp(newCigarString.c_str(), "8S1M") == 0);
304
305 record.setCigar(origCigar);
306 assert(CigarHelper::softClipBeginByRefPos(record, 18, newCigar, newPos) == 8);
307 assert(newPos == 10);
308 newCigar.getCigarString(newCigarString);
309 //std::cout << newCigarString.c_str() << std::endl;
310 assert(strcmp(newCigarString.c_str(), "9S") == 0);
311
312 record.setCigar(origCigar);
313 assert(CigarHelper::softClipBeginByRefPos(record, 19, newCigar, newPos) == 8);
314 assert(newPos == 10);
315 newCigar.getCigarString(newCigarString);
316 //std::cout << newCigarString.c_str() << std::endl;
317 assert(strcmp(newCigarString.c_str(), "9S") == 0);
318
319 ////////////////////////////////////////////////////////
320 ////////////////////////////////////////////////////////
321 // Test clipping at every position when first non-clip instruction is delete.
322 origCigar = "3H3S3D3M3S3H";
323 record.setCigar(origCigar);
324 record.setSequence("gggAAAggg");
325 // Cigar: HHHSSSDDDMMMSSSHHH
326 // ReadPos: 000 000000
327 // ReadPos: 012 345678
328 // RefPos: 111111
329 // RefPos: 012345
330 record.setCigar(origCigar);
331 assert(CigarHelper::softClipBeginByRefPos(record, 9, newCigar, newPos) ==
332 CigarHelper::NO_CLIP);
333 assert(newPos == 10);
334 newCigar.getCigarString(newCigarString);
335 //std::cout << newCigarString.c_str() << std::endl;
336 assert(strcmp(newCigarString.c_str(), origCigar) == 0);
337
338 record.setCigar(origCigar);
339 assert(CigarHelper::softClipBeginByRefPos(record, 10, newCigar, newPos) == 2);
340 assert(newPos == 13);
341 newCigar.getCigarString(newCigarString);
342 //std::cout << newCigarString.c_str() << std::endl;
343 assert(strcmp(newCigarString.c_str(), "3H3S3M3S3H") == 0);
344
345 record.setCigar(origCigar);
346 assert(CigarHelper::softClipBeginByRefPos(record, 11, newCigar, newPos) == 2);
347 assert(newPos == 13);
348 newCigar.getCigarString(newCigarString);
349 //std::cout << newCigarString.c_str() << std::endl;
350 assert(strcmp(newCigarString.c_str(), "3H3S3M3S3H") == 0);
351
352 record.setCigar(origCigar);
353 assert(CigarHelper::softClipBeginByRefPos(record, 12, newCigar, newPos) == 2);
354 assert(newPos == 13);
355 newCigar.getCigarString(newCigarString);
356 //std::cout << newCigarString.c_str() << std::endl;
357 assert(strcmp(newCigarString.c_str(), "3H3S3M3S3H") == 0);
358
359 record.setCigar(origCigar);
360 assert(CigarHelper::softClipBeginByRefPos(record, 13, newCigar, newPos) == 3);
361 assert(newPos == 14);
362 newCigar.getCigarString(newCigarString);
363 //std::cout << newCigarString.c_str() << std::endl;
364 assert(strcmp(newCigarString.c_str(), "3H4S2M3S3H") == 0);
365
366 record.setCigar(origCigar);
367 assert(CigarHelper::softClipBeginByRefPos(record, 14, newCigar, newPos) == 4);
368 assert(newPos == 15);
369 newCigar.getCigarString(newCigarString);
370 //std::cout << newCigarString.c_str() << std::endl;
371 assert(strcmp(newCigarString.c_str(), "3H5S1M3S3H") == 0);
372
373 record.setCigar(origCigar);
374 assert(CigarHelper::softClipBeginByRefPos(record, 15, newCigar, newPos) == 8);
375 assert(newPos == 10);
376 newCigar.getCigarString(newCigarString);
377 //std::cout << newCigarString.c_str() << std::endl;
378 assert(strcmp(newCigarString.c_str(), "3H9S3H") == 0);
379
380 record.setCigar(origCigar);
381 assert(CigarHelper::softClipBeginByRefPos(record, 16, newCigar, newPos) == 8);
382 assert(newPos == 10);
383 newCigar.getCigarString(newCigarString);
384 //std::cout << newCigarString.c_str() << std::endl;
385 assert(strcmp(newCigarString.c_str(), "3H9S3H") == 0);
386
387 ////////////////////////////////////////////////////////
388 ////////////////////////////////////////////////////////
389 // Test clipping at every position when first non-clip instruction is insert.
390 origCigar = "3H3S3I3M3S3H";
391 record.setCigar(origCigar);
392 record.setSequence("gggAAATTTggg");
393 // Cigar: HHHSSSIIIMMMSSSHHH
394 // ReadPos: 000000000011
395 // ReadPos: 012345678901
396 // RefPos: 111
397 // RefPos: 012
398 record.setCigar(origCigar);
399 assert(CigarHelper::softClipBeginByRefPos(record, 9, newCigar, newPos) ==
400 CigarHelper::NO_CLIP);
401 assert(newPos == 10);
402 newCigar.getCigarString(newCigarString);
403 //std::cout << newCigarString.c_str() << std::endl;
404 assert(strcmp(newCigarString.c_str(), origCigar) == 0);
405
406 record.setCigar(origCigar);
407 assert(CigarHelper::softClipBeginByRefPos(record, 10, newCigar, newPos) == 6);
408 assert(newPos == 11);
409 newCigar.getCigarString(newCigarString);
410 //std::cout << newCigarString.c_str() << std::endl;
411 assert(strcmp(newCigarString.c_str(), "3H7S2M3S3H") == 0);
412
413 record.setCigar(origCigar);
414 assert(CigarHelper::softClipBeginByRefPos(record, 11, newCigar, newPos) == 7);
415 assert(newPos == 12);
416 newCigar.getCigarString(newCigarString);
417 //std::cout << newCigarString.c_str() << std::endl;
418 assert(strcmp(newCigarString.c_str(), "3H8S1M3S3H") == 0);
419
420 record.setCigar(origCigar);
421 assert(CigarHelper::softClipBeginByRefPos(record, 12, newCigar, newPos) == 11);
422 assert(newPos == 10);
423 newCigar.getCigarString(newCigarString);
424 //std::cout << newCigarString.c_str() << std::endl;
425 assert(strcmp(newCigarString.c_str(), "3H12S3H") == 0);
426
427 record.setCigar(origCigar);
428 assert(CigarHelper::softClipBeginByRefPos(record, 13, newCigar, newPos) == 11);
429 assert(newPos == 10);
430 newCigar.getCigarString(newCigarString);
431 //std::cout << newCigarString.c_str() << std::endl;
432 assert(strcmp(newCigarString.c_str(), "3H12S3H") == 0);
433}
434
435
436void CigarHelperTest::testSoftClipEndByRefPos()
437{
438 SamRecord record;
439 CigarRoller newCigar;
440 std::string newCigarString;
441
442 // Setup the current Cigar.
443 // Cigar: HHHSSSMMMDDDMMMIIIMMMPPPMMMDDDMMMSSSHHH
444 // ReadPos: 000000 000011111 111 112222
445 // ReadPos: 012345 678901234 567 890123
446 // RefPos: 111111111 122 222222223
447 // RefPos: 012345678 901 234567890
448 const char* origCigar = "3H3S3M3D3M3I3M3P3M3D3M3S3H";
449 record.setCigar(origCigar);
450 record.set0BasedPosition(10);
451 record.setSequence("gggAAATTTCCCTTTGGGAAAggg");
452
453 ////////////////////////////////////////////////////////
454 // Clip outside of the range (after). Nothing should change.
455 assert(CigarHelper::softClipEndByRefPos(record, 10000, newCigar) ==
456 CigarHelper::NO_CLIP);
457 newCigar.getCigarString(newCigarString);
458 assert(strcmp(newCigarString.c_str(), origCigar) == 0);
459
460 ////////////////////////////////////////////////////////
461 // Clip outside of the range (before). Everything should be clipped.
462 assert(CigarHelper::softClipEndByRefPos(record, 1, newCigar) == 0);
463 newCigar.getCigarString(newCigarString);
464 //std::cout << newCigarString.c_str() << std::endl;
465 assert(strcmp(newCigarString.c_str(), "3H24S3H") == 0);
466
467
468 ////////////////////////////////////////////////////////
469 ////////////////////////////////////////////////////////
470 // Test clipping at every position of the read.
471
472 ////////////////////////////////////////////////////////
473 // Clip at the first position.
474 assert(CigarHelper::softClipEndByRefPos(record, 10, newCigar) == 0);
475 newCigar.getCigarString(newCigarString);
476 //std::cout << newCigarString.c_str() << std::endl;
477 assert(strcmp(newCigarString.c_str(), "3H24S3H") == 0);
478
479 ////////////////////////////////////////////////////////
480 // Clip in the middle of the first Match.
481 assert(CigarHelper::softClipEndByRefPos(record, 11, newCigar) == 4);
482 newCigar.getCigarString(newCigarString);
483 //std::cout << newCigarString.c_str() << std::endl;
484 assert(strcmp(newCigarString.c_str(), "3H3S1M20S3H") == 0);
485
486 ////////////////////////////////////////////////////////
487 // Clip just before the first deletion.
488 assert(CigarHelper::softClipEndByRefPos(record, 12, newCigar) == 5);
489 newCigar.getCigarString(newCigarString);
490 //std::cout << newCigarString.c_str() << std::endl;
491 assert(strcmp(newCigarString.c_str(), "3H3S2M19S3H") == 0);
492
493 ////////////////////////////////////////////////////////
494 // Clip at the first deletion.
495 assert(CigarHelper::softClipEndByRefPos(record, 13, newCigar) == 6);
496 newCigar.getCigarString(newCigarString);
497 //std::cout << newCigarString.c_str() << std::endl;
498 assert(strcmp(newCigarString.c_str(), "3H3S3M18S3H") == 0);
499
500 ////////////////////////////////////////////////////////
501 // Clip in the middle of the first deletion.
502 assert(CigarHelper::softClipEndByRefPos(record, 14, newCigar) == 6);
503 newCigar.getCigarString(newCigarString);
504 //std::cout << newCigarString.c_str() << std::endl;
505 assert(strcmp(newCigarString.c_str(), "3H3S3M18S3H") == 0);
506
507 ////////////////////////////////////////////////////////
508 // Clip in the end of the first deletion.
509 assert(CigarHelper::softClipEndByRefPos(record, 15, newCigar) == 6);
510 newCigar.getCigarString(newCigarString);
511 //std::cout << newCigarString.c_str() << std::endl;
512 assert(strcmp(newCigarString.c_str(), "3H3S3M18S3H") == 0);
513
514 ////////////////////////////////////////////////////////
515 // Clip just after the first deletion (should remove the deletion).
516 assert(CigarHelper::softClipEndByRefPos(record, 16, newCigar) == 6);
517 newCigar.getCigarString(newCigarString);
518 //std::cout << newCigarString.c_str() << std::endl;
519 assert(strcmp(newCigarString.c_str(), "3H3S3M18S3H") == 0);
520
521 ////////////////////////////////////////////////////////
522 // Clip in middle of read after 1st deletion.
523 assert(CigarHelper::softClipEndByRefPos(record, 17, newCigar) == 7);
524 newCigar.getCigarString(newCigarString);
525 //std::cout << newCigarString.c_str() << std::endl;
526 assert(strcmp(newCigarString.c_str(), "3H3S3M3D1M17S3H") == 0);
527
528 ////////////////////////////////////////////////////////
529 // Clip in middle of read after 1st deletion.
530 assert(CigarHelper::softClipEndByRefPos(record, 18, newCigar) == 8);
531 newCigar.getCigarString(newCigarString);
532 //std::cout << newCigarString.c_str() << std::endl;
533 assert(strcmp(newCigarString.c_str(), "3H3S3M3D2M16S3H") == 0);
534
535 ////////////////////////////////////////////////////////
536 // Clip just after the 1st insertion.
537 assert(CigarHelper::softClipEndByRefPos(record, 19, newCigar) == 12);
538 newCigar.getCigarString(newCigarString);
539 //std::cout << newCigarString.c_str() << std::endl;
540 assert(strcmp(newCigarString.c_str(), "3H3S3M3D3M3I12S3H") == 0);
541
542 ////////////////////////////////////////////////////////
543 // Clip in middle of the match after 1st insertion.
544 assert(CigarHelper::softClipEndByRefPos(record, 20, newCigar) == 13);
545 newCigar.getCigarString(newCigarString);
546 //std::cout << newCigarString.c_str() << std::endl;
547 assert(strcmp(newCigarString.c_str(), "3H3S3M3D3M3I1M11S3H") == 0);
548
549 ////////////////////////////////////////////////////////
550 // Clip in middle of the match after 1st insertion.
551 assert(CigarHelper::softClipEndByRefPos(record, 21, newCigar) == 14);
552 newCigar.getCigarString(newCigarString);
553 //std::cout << newCigarString.c_str() << std::endl;
554 assert(strcmp(newCigarString.c_str(), "3H3S3M3D3M3I2M10S3H") == 0);
555
556 ////////////////////////////////////////////////////////
557 // Clip right after the pad
558 assert(CigarHelper::softClipEndByRefPos(record, 22, newCigar) == 15);
559 newCigar.getCigarString(newCigarString);
560 //std::cout << newCigarString.c_str() << std::endl;
561 assert(strcmp(newCigarString.c_str(), "3H3S3M3D3M3I3M9S3H") == 0);
562
563 ////////////////////////////////////////////////////////
564 // Clip middle of read after the pad
565 assert(CigarHelper::softClipEndByRefPos(record, 23, newCigar) == 16);
566 newCigar.getCigarString(newCigarString);
567 //std::cout << newCigarString.c_str() << std::endl;
568 assert(strcmp(newCigarString.c_str(), "3H3S3M3D3M3I3M3P1M8S3H") == 0);
569
570 ////////////////////////////////////////////////////////
571 // Clip end of read after the pad before deletion
572 assert(CigarHelper::softClipEndByRefPos(record, 24, newCigar) == 17);
573 newCigar.getCigarString(newCigarString);
574 //std::cout << newCigarString.c_str() << std::endl;
575 assert(strcmp(newCigarString.c_str(), "3H3S3M3D3M3I3M3P2M7S3H") == 0);
576
577 ////////////////////////////////////////////////////////
578 // Clip at start of 2nd deletion.
579 assert(CigarHelper::softClipEndByRefPos(record, 25, newCigar) == 18);
580 newCigar.getCigarString(newCigarString);
581 //std::cout << newCigarString.c_str() << std::endl;
582 assert(strcmp(newCigarString.c_str(), "3H3S3M3D3M3I3M3P3M6S3H") == 0);
583
584 ////////////////////////////////////////////////////////
585 // Clip in 2nd deletion.
586 assert(CigarHelper::softClipEndByRefPos(record, 26, newCigar) == 18);
587 newCigar.getCigarString(newCigarString);
588 //std::cout << newCigarString.c_str() << std::endl;
589 assert(strcmp(newCigarString.c_str(), "3H3S3M3D3M3I3M3P3M6S3H") == 0);
590
591 ////////////////////////////////////////////////////////
592 // Clip in 2nd deletion.
593 assert(CigarHelper::softClipEndByRefPos(record, 27, newCigar) == 18);
594 newCigar.getCigarString(newCigarString);
595 //std::cout << newCigarString.c_str() << std::endl;
596 assert(strcmp(newCigarString.c_str(), "3H3S3M3D3M3I3M3P3M6S3H") == 0);
597
598 ////////////////////////////////////////////////////////
599 // Clip right after 2nd deletion.
600 assert(CigarHelper::softClipEndByRefPos(record, 28, newCigar) == 18);
601 newCigar.getCigarString(newCigarString);
602 //std::cout << newCigarString.c_str() << std::endl;
603 assert(strcmp(newCigarString.c_str(), "3H3S3M3D3M3I3M3P3M6S3H") == 0);
604
605 ////////////////////////////////////////////////////////
606 // Clip in middle of last match.
607 assert(CigarHelper::softClipEndByRefPos(record, 29, newCigar) == 19);
608 newCigar.getCigarString(newCigarString);
609 //std::cout << newCigarString.c_str() << std::endl;
610 assert(strcmp(newCigarString.c_str(), "3H3S3M3D3M3I3M3P3M3D1M5S3H") == 0);
611
612 ////////////////////////////////////////////////////////
613 // Clip in middle of last match.
614 assert(CigarHelper::softClipEndByRefPos(record, 30, newCigar) == 20);
615 newCigar.getCigarString(newCigarString);
616 //std::cout << newCigarString.c_str() << std::endl;
617 assert(strcmp(newCigarString.c_str(), "3H3S3M3D3M3I3M3P3M3D2M4S3H") == 0);
618
619 ////////////////////////////////////////////////////////
620 // Clip right after the read (no change).
621 assert(CigarHelper::softClipEndByRefPos(record, 31, newCigar) ==
622 CigarHelper::NO_CLIP);
623 newCigar.getCigarString(newCigarString);
624 //std::cout << newCigarString.c_str() << std::endl;
625 assert(strcmp(newCigarString.c_str(), origCigar) == 0);
626
627 ////////////////////////////////////////////////////////
628 ////////////////////////////////////////////////////////
629 // Test clipping at every position when insertions & deletions
630 // are next to each other.
631 origCigar = "3M3D3I3M";
632 record.setCigar(origCigar);
633 record.setSequence("GGGAAAGGG");
634 // Cigar: MMMDDDIIIMMM
635 // ReadPos: 000 000000
636 // ReadPos: 012 345678
637 // RefPos: 111111 111
638 // RefPos: 012345 678
639 record.setCigar(origCigar);
640 assert(CigarHelper::softClipEndByRefPos(record, 9, newCigar) == 0);
641 newCigar.getCigarString(newCigarString);
642 //std::cout << newCigarString.c_str() << std::endl;
643 assert(strcmp(newCigarString.c_str(), "9S") == 0);
644
645 record.setCigar(origCigar);
646 assert(CigarHelper::softClipEndByRefPos(record, 10, newCigar) == 0);
647 newCigar.getCigarString(newCigarString);
648 //std::cout << newCigarString.c_str() << std::endl;
649 assert(strcmp(newCigarString.c_str(), "9S") == 0);
650
651 record.setCigar(origCigar);
652 assert(CigarHelper::softClipEndByRefPos(record, 11, newCigar) == 1);
653 newCigar.getCigarString(newCigarString);
654 //std::cout << newCigarString.c_str() << std::endl;
655 assert(strcmp(newCigarString.c_str(), "1M8S") == 0);
656
657 record.setCigar(origCigar);
658 assert(CigarHelper::softClipEndByRefPos(record, 12, newCigar) == 2);
659 newCigar.getCigarString(newCigarString);
660 //std::cout << newCigarString.c_str() << std::endl;
661 assert(strcmp(newCigarString.c_str(), "2M7S") == 0);
662
663 record.setCigar(origCigar);
664 assert(CigarHelper::softClipEndByRefPos(record, 13, newCigar) == 3);
665 newCigar.getCigarString(newCigarString);
666 //std::cout << newCigarString.c_str() << std::endl;
667 assert(strcmp(newCigarString.c_str(), "3M6S") == 0);
668
669 record.setCigar(origCigar);
670 assert(CigarHelper::softClipEndByRefPos(record, 14, newCigar) == 3);
671 newCigar.getCigarString(newCigarString);
672 //std::cout << newCigarString.c_str() << std::endl;
673 assert(strcmp(newCigarString.c_str(), "3M6S") == 0);
674
675 record.setCigar(origCigar);
676 assert(CigarHelper::softClipEndByRefPos(record, 15, newCigar) == 3);
677 newCigar.getCigarString(newCigarString);
678 //std::cout << newCigarString.c_str() << std::endl;
679 assert(strcmp(newCigarString.c_str(), "3M6S") == 0);
680
681 record.setCigar(origCigar);
682 assert(CigarHelper::softClipEndByRefPos(record, 16, newCigar) == 6);
683 newCigar.getCigarString(newCigarString);
684 //std::cout << newCigarString.c_str() << std::endl;
685 assert(strcmp(newCigarString.c_str(), "3M3D3I3S") == 0);
686
687 record.setCigar(origCigar);
688 assert(CigarHelper::softClipEndByRefPos(record, 17, newCigar) == 7);
689 newCigar.getCigarString(newCigarString);
690 //std::cout << newCigarString.c_str() << std::endl;
691 assert(strcmp(newCigarString.c_str(), "3M3D3I1M2S") == 0);
692
693 record.setCigar(origCigar);
694 assert(CigarHelper::softClipEndByRefPos(record, 18, newCigar) == 8);
695 newCigar.getCigarString(newCigarString);
696 //std::cout << newCigarString.c_str() << std::endl;
697 assert(strcmp(newCigarString.c_str(), "3M3D3I2M1S") == 0);
698
699 record.setCigar(origCigar);
700 assert(CigarHelper::softClipEndByRefPos(record, 19, newCigar) ==
701 CigarHelper::NO_CLIP);
702 newCigar.getCigarString(newCigarString);
703 //std::cout << newCigarString.c_str() << std::endl;
704 assert(strcmp(newCigarString.c_str(), origCigar) == 0);
705
706 ////////////////////////////////////////////////////////
707 ////////////////////////////////////////////////////////
708 // Test clipping at every position when first non-clip instruction is delete.
709 origCigar = "3H3S3D3M3S3H";
710 record.setCigar(origCigar);
711 record.setSequence("gggAAAggg");
712 // Cigar: HHHSSSDDDMMMSSSHHH
713 // ReadPos: 000 000000
714 // ReadPos: 012 345678
715 // RefPos: 111111
716 // RefPos: 012345
717 record.setCigar(origCigar);
718 assert(CigarHelper::softClipEndByRefPos(record, 9, newCigar) == 0);
719 newCigar.getCigarString(newCigarString);
720 //std::cout << newCigarString.c_str() << std::endl;
721 assert(strcmp(newCigarString.c_str(), "3H9S3H") == 0);
722
723 record.setCigar(origCigar);
724 assert(CigarHelper::softClipEndByRefPos(record, 10, newCigar) == 0);
725 newCigar.getCigarString(newCigarString);
726 //std::cout << newCigarString.c_str() << std::endl;
727 assert(strcmp(newCigarString.c_str(), "3H9S3H") == 0);
728
729 record.setCigar(origCigar);
730 assert(CigarHelper::softClipEndByRefPos(record, 11, newCigar) == 0);
731 newCigar.getCigarString(newCigarString);
732 //std::cout << newCigarString.c_str() << std::endl;
733 assert(strcmp(newCigarString.c_str(), "3H9S3H") == 0);
734
735 record.setCigar(origCigar);
736 assert(CigarHelper::softClipEndByRefPos(record, 12, newCigar) == 0);
737 newCigar.getCigarString(newCigarString);
738 //std::cout << newCigarString.c_str() << std::endl;
739 assert(strcmp(newCigarString.c_str(), "3H9S3H") == 0);
740
741 record.setCigar(origCigar);
742 assert(CigarHelper::softClipEndByRefPos(record, 13, newCigar) == 0);
743 newCigar.getCigarString(newCigarString);
744 //std::cout << newCigarString.c_str() << std::endl;
745 assert(strcmp(newCigarString.c_str(), "3H9S3H") == 0);
746
747 record.setCigar(origCigar);
748 assert(CigarHelper::softClipEndByRefPos(record, 14, newCigar) == 4);
749 newCigar.getCigarString(newCigarString);
750 //std::cout << newCigarString.c_str() << std::endl;
751 assert(strcmp(newCigarString.c_str(), "3H3S3D1M5S3H") == 0);
752
753 record.setCigar(origCigar);
754 assert(CigarHelper::softClipEndByRefPos(record, 15, newCigar) == 5);
755 newCigar.getCigarString(newCigarString);
756 //std::cout << newCigarString.c_str() << std::endl;
757 assert(strcmp(newCigarString.c_str(), "3H3S3D2M4S3H") == 0);
758
759 record.setCigar(origCigar);
760 assert(CigarHelper::softClipEndByRefPos(record, 16, newCigar) ==
761 CigarHelper::NO_CLIP);
762 newCigar.getCigarString(newCigarString);
763 //std::cout << newCigarString.c_str() << std::endl;
764 assert(strcmp(newCigarString.c_str(), origCigar) == 0);
765
766 ////////////////////////////////////////////////////////
767 ////////////////////////////////////////////////////////
768 // Test clipping at every position when first non-clip instruction is insert.
769 origCigar = "3H3S3I3M3S3H";
770 record.setCigar(origCigar);
771 record.setSequence("gggAAATTTggg");
772 // Cigar: HHHSSSIIIMMMSSSHHH
773 // ReadPos: 000000000011
774 // ReadPos: 012345678901
775 // RefPos: 111
776 // RefPos: 012
777 record.setCigar(origCigar);
778 assert(CigarHelper::softClipEndByRefPos(record, 9, newCigar) == 0);
779 newCigar.getCigarString(newCigarString);
780 //std::cout << newCigarString.c_str() << std::endl;
781 assert(strcmp(newCigarString.c_str(), "3H12S3H") == 0);
782
783 record.setCigar(origCigar);
784 assert(CigarHelper::softClipEndByRefPos(record, 10, newCigar) == 6);
785 newCigar.getCigarString(newCigarString);
786 //std::cout << newCigarString.c_str() << std::endl;
787 assert(strcmp(newCigarString.c_str(), "3H3S3I6S3H") == 0);
788
789 record.setCigar(origCigar);
790 assert(CigarHelper::softClipEndByRefPos(record, 11, newCigar) == 7);
791 newCigar.getCigarString(newCigarString);
792 //std::cout << newCigarString.c_str() << std::endl;
793 assert(strcmp(newCigarString.c_str(), "3H3S3I1M5S3H") == 0);
794
795 record.setCigar(origCigar);
796 assert(CigarHelper::softClipEndByRefPos(record, 12, newCigar) == 8);
797 newCigar.getCigarString(newCigarString);
798 //std::cout << newCigarString.c_str() << std::endl;
799 assert(strcmp(newCigarString.c_str(), "3H3S3I2M4S3H") == 0);
800
801 record.setCigar(origCigar);
802 assert(CigarHelper::softClipEndByRefPos(record, 13, newCigar) ==
803 CigarHelper::NO_CLIP);
804 newCigar.getCigarString(newCigarString);
805 //std::cout << newCigarString.c_str() << std::endl;
806 assert(strcmp(newCigarString.c_str(), origCigar) == 0);
807}
CigarHelper::softClipBeginByRefPos
static int32_t softClipBeginByRefPos(SamRecord &record, int32_t refPosition0Based, CigarRoller &newCigar, int32_t &new0BasedPosition)
Soft clip the cigar from the beginning of the read at the specified reference position.
Definition CigarHelper.cpp:23
CigarHelper::softClipEndByRefPos
static int32_t softClipEndByRefPos(SamRecord &record, int32_t refPosition0Based, CigarRoller &newCigar)
Soft clip the cigar from the back of the read at the specified reference position.
Definition CigarHelper.cpp:184
Cigar::getCigarString
void getCigarString(String &cigarString) const
Set the passed in String to the string reprentation of the Cigar operations in this object.
Definition Cigar.cpp:52
SamRecord::setCigar
bool setCigar(const char *cigar)
Set the CIGAR to the specified SAM formatted cigar string.
Definition SamRecord.cpp:259
SamRecord::setSequence
bool setSequence(const char *seq)
Sets the sequence (SEQ) to the specified SAM formatted sequence string.
Definition SamRecord.cpp:344
SamRecord::set0BasedPosition
bool set0BasedPosition(int32_t position)
Set the leftmost position using the specified 0-based (BAM format) value.
Definition SamRecord.cpp:242