21const String FIRST_SEQID_LINE =
"@Valid with comment";
22const String FIRST_SEQID =
"Valid";
23const String FIRST_RAW_SEQ =
"ACTGNactng.0123";
24const String FIRST_PLUS_LINE =
"+";
25const String FIRST_QUALITY =
"!#\"$%&'()*+,-./";
26const String SECOND_SEQID_LINE =
"@Valid1 with comment";
27const String SECOND_SEQID =
"Valid1";
28const String SECOND_RAW_SEQ =
"ACTGACTNactngaac";
29const String SECOND_PLUS_LINE =
"+";
30const String SECOND_QUALITY =
"0123456789:;<=>@";
31const String THIRD_SEQID_LINE =
"@Valid2";
32const String THIRD_SEQID =
"Valid2";
33const String THIRD_RAW_SEQ =
"A123.0321.011";
34const String THIRD_PLUS_LINE =
"+";
35const String THIRD_QUALITY =
"?@ABCDEFGHIJK";
36const String FOURTH_SEQID_LINE =
"@Valid3";
37const String FOURTH_SEQID =
"Valid3";
38const String FOURTH_RAW_SEQ =
"ACTGACTNactngACTGACTNactng";
39const String FOURTH_PLUS_LINE =
"+";
40const String FOURTH_QUALITY =
"LMNOPQRSTUVWXYZ[\\]^_'abcde";
41const String FIFTH_SEQID_LINE =
"@Valid4";
42const String FIFTH_SEQID =
"Valid4";
43const String FIFTH_RAW_SEQ =
"ACTGACTNactngACTGACTNactng";
44const String FIFTH_PLUS_LINE =
"+";
45const String FIFTH_QUALITY =
"fghijklmnopqrstuvwxyz{|}~~";
46const String SIXTH_SEQID_LINE =
"@";
47const String SIXTH_SEQID =
"";
48const String SIXTH_RAW_SEQ =
"ACTGACTNactng";
49const String SIXTH_PLUS_LINE =
"+";
50const String SIXTH_QUALITY =
"?@ABCDEFGHIJK";
51const String SEVENTH_SEQID_LINE =
"Line no start with @";
52const String SEVENTH_SEQID =
"";
53const String SEVENTH_RAW_SEQ =
"ACTGACTNactng";
54const String SEVENTH_PLUS_LINE =
"+";
55const String SEVENTH_QUALITY =
"LMNOPQRSTUVWX";
56const String EIGHTH_SEQID_LINE =
"@ a";
57const String EIGHTH_SEQID =
"";
58const String EIGHTH_RAW_SEQ =
"ACTGACTNactng";
59const String EIGHTH_PLUS_LINE =
"+";
60const String EIGHTH_QUALITY =
"YZ[\\]^_'abcde";
61const String NINTH_SEQID_LINE =
"@ ";
62const String NINTH_SEQID =
"";
63const String NINTH_RAW_SEQ =
"ACTGACTNactng";
64const String NINTH_PLUS_LINE =
"+";
65const String NINTH_QUALITY =
"fghijklmnopqr";
66const String TENTH_SEQID_LINE =
"@Valid";
67const String TENTH_SEQID =
"Valid";
68const String TENTH_RAW_SEQ =
"ACTGNactng";
69const String TENTH_PLUS_LINE =
"+";
70const String TENTH_QUALITY =
"!#\"$%&'()*";
71const String ELEVENTH_SEQID_LINE =
"@RawError1";
72const String ELEVENTH_SEQID =
"RawError1";
73const String ELEVENTH_RAW_SEQ =
"ACTNaHtng0aBZa";
74const String ELEVENTH_PLUS_LINE =
"+";
75const String ELEVENTH_QUALITY =
"ACTNactng0aBaZ";
76const String TWELFTH_SEQID_LINE =
"@RawError2";
77const String TWELFTH_SEQID =
"RawError2";
78const String TWELFTH_RAW_SEQ =
"aaa";
79const String TWELFTH_PLUS_LINE =
"+";
80const String TWELFTH_QUALITY =
"aaa";
81const String THIRTEENTH_SEQID_LINE =
"@RawError3";
82const String THIRTEENTH_SEQID =
"RawError3";
83const String THIRTEENTH_RAW_SEQ =
"ACTGACTNactng";
84const String THIRTEENTH_PLUS_LINE =
"+";
85const String THIRTEENTH_QUALITY =
"ACTGACTNactng";
86const String FOURTEENTH_SEQID_LINE =
"@QualityError1";
87const String FOURTEENTH_SEQID =
"QualityError1";
88const String FOURTEENTH_RAW_SEQ =
"ACTGCacgnc";
89const String FOURTEENTH_PLUS_LINE =
"+";
90const String FOURTEENTH_QUALITY =
"ac gcacg n";
91const String FIFTEENTH_SEQID_LINE =
"@QualityError2";
92const String FIFTEENTH_SEQID =
"QualityError2";
93const String FIFTEENTH_RAW_SEQ =
"ACTGCacgnc";
94const String FIFTEENTH_PLUS_LINE =
"+";
95const String FIFTEENTH_QUALITY =
"actgc@cgnc";
96const String SIXTEENTH_SEQID_LINE =
"@QualityError3";
97const String SIXTEENTH_SEQID =
"QualityError3";
98const String SIXTEENTH_RAW_SEQ =
"ACTGCacgnc";
99const String SIXTEENTH_PLUS_LINE =
"+";
100const String SIXTEENTH_QUALITY =
"actgc77acgnc";
101const String SEVENTEENTH_SEQID_LINE =
"@PlusValid1";
102const String SEVENTEENTH_SEQID =
"PlusValid1";
103const String SEVENTEENTH_RAW_SEQ =
"ACTGCacgnc";
104const String SEVENTEENTH_PLUS_LINE =
"+PlusValid1";
105const String SEVENTEENTH_QUALITY =
"actgcacgnc";
106const String EIGHTEENTH_SEQID_LINE =
"@PlusValid2";
107const String EIGHTEENTH_SEQID =
"PlusValid2";
108const String EIGHTEENTH_RAW_SEQ =
"ACTGCacgnc";
109const String EIGHTEENTH_PLUS_LINE =
"+PlusValid2 Added comment";
110const String EIGHTEENTH_QUALITY =
"actgcacgnc";
111const String NINETEENTH_SEQID_LINE =
"@PlusError1";
112const String NINETEENTH_SEQID =
"PlusError1";
113const String NINETEENTH_RAW_SEQ =
"ACTGCacgnc";
114const String NINETEENTH_PLUS_LINE =
"+PlusError2";
115const String NINETEENTH_QUALITY =
"actgcacgnc";
117const String TWENTIETH_SEQID_LINE =
"@InvalidColor";
118const String TWENTIETH_SEQID =
"InvalidColor";
119const String TWENTIETH_RAW_SEQ =
"0123.0321.011";
120const String TWENTIETH_PLUS_LINE =
"+";
121const String TWENTIETH_QUALITY =
"0123.0321.011";
124const String TWENTY_FIRST_SEQID_LINE =
"@PlusError2";
125const String TWENTY_FIRST_SEQID =
"PlusError2";
126const String TWENTY_FIRST_RAW_SEQ =
"ACTGCacgnc";
127const String TWENTY_FIRST_PLUS_LINE =
"";
128const String TWENTY_FIRST_QUALITY =
"";
130void testReadUnOpenedFile()
134 assert(fastqfile.
isOpen() ==
false);
136 assert(fastqfile.
isOpen() ==
false);
144 assert(fastqfile.
isOpen() ==
false);
146 assert(fastqfile.
isOpen() ==
false);
157 assert(fastqfile.
isOpen() ==
false);
159 assert(fastqfile.
isOpen() ==
false);
163void testReadSequence()
167 assert(fastqfile.
isOpen() ==
false);
170 assert(fastqfile.
isOpen() ==
true);
176 assert(fastqfile.mySequenceIdLine == FIRST_SEQID_LINE);
177 assert(fastqfile.mySequenceIdentifier == FIRST_SEQID);
178 assert(fastqfile.myRawSequence == FIRST_RAW_SEQ);
179 assert(fastqfile.myPlusLine == FIRST_PLUS_LINE);
180 assert(fastqfile.myQualityString == FIRST_QUALITY);
184 assert(fastqfile.mySequenceIdLine == SECOND_SEQID_LINE);
185 assert(fastqfile.mySequenceIdentifier == SECOND_SEQID);
186 assert(fastqfile.myRawSequence == SECOND_RAW_SEQ);
187 assert(fastqfile.myPlusLine == SECOND_PLUS_LINE);
188 assert(fastqfile.myQualityString == SECOND_QUALITY);
191 assert(fastqfile.mySequenceIdLine == THIRD_SEQID_LINE);
192 assert(fastqfile.mySequenceIdentifier == THIRD_SEQID);
193 assert(fastqfile.myRawSequence == THIRD_RAW_SEQ);
194 assert(fastqfile.myPlusLine == THIRD_PLUS_LINE);
195 assert(fastqfile.myQualityString == THIRD_QUALITY);
198 assert(fastqfile.mySequenceIdLine == FOURTH_SEQID_LINE);
199 assert(fastqfile.mySequenceIdentifier == FOURTH_SEQID);
200 assert(fastqfile.myRawSequence == FOURTH_RAW_SEQ);
201 assert(fastqfile.myPlusLine == FOURTH_PLUS_LINE);
202 assert(fastqfile.myQualityString == FOURTH_QUALITY);
205 assert(fastqfile.mySequenceIdLine == FIFTH_SEQID_LINE);
206 assert(fastqfile.mySequenceIdentifier == FIFTH_SEQID);
207 assert(fastqfile.myRawSequence == FIFTH_RAW_SEQ);
208 assert(fastqfile.myPlusLine == FIFTH_PLUS_LINE);
209 assert(fastqfile.myQualityString == FIFTH_QUALITY);
212 assert(fastqfile.mySequenceIdLine == SIXTH_SEQID_LINE);
213 assert(fastqfile.mySequenceIdentifier == SIXTH_SEQID);
214 assert(fastqfile.myRawSequence == SIXTH_RAW_SEQ);
215 assert(fastqfile.myPlusLine == SIXTH_PLUS_LINE);
216 assert(fastqfile.myQualityString == SIXTH_QUALITY);
219 assert(fastqfile.mySequenceIdLine == SEVENTH_SEQID_LINE);
220 assert(fastqfile.mySequenceIdentifier == SEVENTH_SEQID);
221 assert(fastqfile.myRawSequence == SEVENTH_RAW_SEQ);
222 assert(fastqfile.myPlusLine == SEVENTH_PLUS_LINE);
223 assert(fastqfile.myQualityString == SEVENTH_QUALITY);
226 assert(fastqfile.mySequenceIdLine == EIGHTH_SEQID_LINE);
227 assert(fastqfile.mySequenceIdentifier == EIGHTH_SEQID);
228 assert(fastqfile.myRawSequence == EIGHTH_RAW_SEQ);
229 assert(fastqfile.myPlusLine == EIGHTH_PLUS_LINE);
230 assert(fastqfile.myQualityString == EIGHTH_QUALITY);
233 assert(fastqfile.mySequenceIdLine == NINTH_SEQID_LINE);
234 assert(fastqfile.mySequenceIdentifier == NINTH_SEQID);
235 assert(fastqfile.myRawSequence == NINTH_RAW_SEQ);
236 assert(fastqfile.myPlusLine == NINTH_PLUS_LINE);
237 assert(fastqfile.myQualityString == NINTH_QUALITY);
240 assert(fastqfile.mySequenceIdLine == TENTH_SEQID_LINE);
241 assert(fastqfile.mySequenceIdentifier == TENTH_SEQID);
242 assert(fastqfile.myRawSequence == TENTH_RAW_SEQ);
243 assert(fastqfile.myPlusLine == TENTH_PLUS_LINE);
244 assert(fastqfile.myQualityString == TENTH_QUALITY);
247 assert(fastqfile.mySequenceIdLine == ELEVENTH_SEQID_LINE);
248 assert(fastqfile.mySequenceIdentifier == ELEVENTH_SEQID);
249 assert(fastqfile.myRawSequence == ELEVENTH_RAW_SEQ);
250 assert(fastqfile.myPlusLine == ELEVENTH_PLUS_LINE);
251 assert(fastqfile.myQualityString == ELEVENTH_QUALITY);
254 assert(fastqfile.mySequenceIdLine == TWELFTH_SEQID_LINE);
255 assert(fastqfile.mySequenceIdentifier == TWELFTH_SEQID);
256 assert(fastqfile.myRawSequence == TWELFTH_RAW_SEQ);
257 assert(fastqfile.myPlusLine == TWELFTH_PLUS_LINE);
258 assert(fastqfile.myQualityString == TWELFTH_QUALITY);
261 assert(fastqfile.mySequenceIdLine == THIRTEENTH_SEQID_LINE);
262 assert(fastqfile.mySequenceIdentifier == THIRTEENTH_SEQID);
263 assert(fastqfile.myRawSequence == THIRTEENTH_RAW_SEQ);
264 assert(fastqfile.myPlusLine == THIRTEENTH_PLUS_LINE);
265 assert(fastqfile.myQualityString == THIRTEENTH_QUALITY);
268 assert(fastqfile.mySequenceIdLine == FOURTEENTH_SEQID_LINE);
269 assert(fastqfile.mySequenceIdentifier == FOURTEENTH_SEQID);
270 assert(fastqfile.myRawSequence == FOURTEENTH_RAW_SEQ);
271 assert(fastqfile.myPlusLine == FOURTEENTH_PLUS_LINE);
272 assert(fastqfile.myQualityString == FOURTEENTH_QUALITY);
275 assert(fastqfile.mySequenceIdLine == FIFTEENTH_SEQID_LINE);
276 assert(fastqfile.mySequenceIdentifier == FIFTEENTH_SEQID);
277 assert(fastqfile.myRawSequence == FIFTEENTH_RAW_SEQ);
278 assert(fastqfile.myPlusLine == FIFTEENTH_PLUS_LINE);
279 assert(fastqfile.myQualityString == FIFTEENTH_QUALITY);
282 assert(fastqfile.mySequenceIdLine == SIXTEENTH_SEQID_LINE);
283 assert(fastqfile.mySequenceIdentifier == SIXTEENTH_SEQID);
284 assert(fastqfile.myRawSequence == SIXTEENTH_RAW_SEQ);
285 assert(fastqfile.myPlusLine == SIXTEENTH_PLUS_LINE);
286 assert(fastqfile.myQualityString == SIXTEENTH_QUALITY);
289 assert(fastqfile.mySequenceIdLine == SEVENTEENTH_SEQID_LINE);
290 assert(fastqfile.mySequenceIdentifier == SEVENTEENTH_SEQID);
291 assert(fastqfile.myRawSequence == SEVENTEENTH_RAW_SEQ);
292 assert(fastqfile.myPlusLine == SEVENTEENTH_PLUS_LINE);
293 assert(fastqfile.myQualityString == SEVENTEENTH_QUALITY);
296 assert(fastqfile.mySequenceIdLine == EIGHTEENTH_SEQID_LINE);
297 assert(fastqfile.mySequenceIdentifier == EIGHTEENTH_SEQID);
298 assert(fastqfile.myRawSequence == EIGHTEENTH_RAW_SEQ);
299 assert(fastqfile.myPlusLine == EIGHTEENTH_PLUS_LINE);
300 assert(fastqfile.myQualityString == EIGHTEENTH_QUALITY);
303 assert(fastqfile.mySequenceIdLine == NINETEENTH_SEQID_LINE);
304 assert(fastqfile.mySequenceIdentifier == NINETEENTH_SEQID);
305 assert(fastqfile.myRawSequence == NINETEENTH_RAW_SEQ);
306 assert(fastqfile.myPlusLine == NINETEENTH_PLUS_LINE);
307 assert(fastqfile.myQualityString == NINETEENTH_QUALITY);
310 assert(fastqfile.mySequenceIdLine == TWENTIETH_SEQID_LINE);
311 assert(fastqfile.mySequenceIdentifier == TWENTIETH_SEQID);
312 assert(fastqfile.myRawSequence == TWENTIETH_RAW_SEQ);
313 assert(fastqfile.myPlusLine == TWENTIETH_PLUS_LINE);
314 assert(fastqfile.myQualityString == TWENTIETH_QUALITY);
317 assert(fastqfile.mySequenceIdLine == TWENTY_FIRST_SEQID_LINE);
318 assert(fastqfile.mySequenceIdentifier == TWENTY_FIRST_SEQID);
319 assert(fastqfile.myRawSequence == TWENTY_FIRST_RAW_SEQ);
320 assert(fastqfile.myPlusLine == TWENTY_FIRST_PLUS_LINE);
321 assert(fastqfile.myQualityString == TWENTY_FIRST_QUALITY);
325 assert(fastqfile.
isOpen() ==
false);
330 assert(fastqfile.
isOpen() ==
false);
333 assert(fastqfile.
isOpen() ==
true);
339 assert(fastqfile.mySequenceIdLine == FIRST_SEQID_LINE);
340 assert(fastqfile.mySequenceIdentifier == FIRST_SEQID);
341 assert(fastqfile.myRawSequence == FIRST_RAW_SEQ);
342 assert(fastqfile.myPlusLine == FIRST_PLUS_LINE);
343 assert(fastqfile.myQualityString == FIRST_QUALITY);
347 assert(fastqfile.mySequenceIdLine == SECOND_SEQID_LINE);
348 assert(fastqfile.mySequenceIdentifier == SECOND_SEQID);
349 assert(fastqfile.myRawSequence == SECOND_RAW_SEQ);
350 assert(fastqfile.myPlusLine == SECOND_PLUS_LINE);
351 assert(fastqfile.myQualityString == SECOND_QUALITY);
354 assert(fastqfile.mySequenceIdLine == THIRD_SEQID_LINE);
355 assert(fastqfile.mySequenceIdentifier == THIRD_SEQID);
356 assert(fastqfile.myRawSequence == THIRD_RAW_SEQ);
357 assert(fastqfile.myPlusLine == THIRD_PLUS_LINE);
358 assert(fastqfile.myQualityString == THIRD_QUALITY);
361 assert(fastqfile.mySequenceIdLine == FOURTH_SEQID_LINE);
362 assert(fastqfile.mySequenceIdentifier == FOURTH_SEQID);
363 assert(fastqfile.myRawSequence == FOURTH_RAW_SEQ);
364 assert(fastqfile.myPlusLine == FOURTH_PLUS_LINE);
365 assert(fastqfile.myQualityString == FOURTH_QUALITY);
368 assert(fastqfile.mySequenceIdLine == FIFTH_SEQID_LINE);
369 assert(fastqfile.mySequenceIdentifier == FIFTH_SEQID);
370 assert(fastqfile.myRawSequence == FIFTH_RAW_SEQ);
371 assert(fastqfile.myPlusLine == FIFTH_PLUS_LINE);
372 assert(fastqfile.myQualityString == FIFTH_QUALITY);
375 assert(fastqfile.mySequenceIdLine == SIXTH_SEQID_LINE);
376 assert(fastqfile.mySequenceIdentifier == SIXTH_SEQID);
377 assert(fastqfile.myRawSequence == SIXTH_RAW_SEQ);
378 assert(fastqfile.myPlusLine == SIXTH_PLUS_LINE);
379 assert(fastqfile.myQualityString == SIXTH_QUALITY);
382 assert(fastqfile.mySequenceIdLine == SEVENTH_SEQID_LINE);
383 assert(fastqfile.mySequenceIdentifier == SEVENTH_SEQID);
384 assert(fastqfile.myRawSequence == SEVENTH_RAW_SEQ);
385 assert(fastqfile.myPlusLine == SEVENTH_PLUS_LINE);
386 assert(fastqfile.myQualityString == SEVENTH_QUALITY);
389 assert(fastqfile.mySequenceIdLine == EIGHTH_SEQID_LINE);
390 assert(fastqfile.mySequenceIdentifier == EIGHTH_SEQID);
391 assert(fastqfile.myRawSequence == EIGHTH_RAW_SEQ);
392 assert(fastqfile.myPlusLine == EIGHTH_PLUS_LINE);
393 assert(fastqfile.myQualityString == EIGHTH_QUALITY);
396 assert(fastqfile.mySequenceIdLine == NINTH_SEQID_LINE);
397 assert(fastqfile.mySequenceIdentifier == NINTH_SEQID);
398 assert(fastqfile.myRawSequence == NINTH_RAW_SEQ);
399 assert(fastqfile.myPlusLine == NINTH_PLUS_LINE);
400 assert(fastqfile.myQualityString == NINTH_QUALITY);
403 assert(fastqfile.mySequenceIdLine == TENTH_SEQID_LINE);
404 assert(fastqfile.mySequenceIdentifier == TENTH_SEQID);
405 assert(fastqfile.myRawSequence == TENTH_RAW_SEQ);
406 assert(fastqfile.myPlusLine == TENTH_PLUS_LINE);
407 assert(fastqfile.myQualityString == TENTH_QUALITY);
410 assert(fastqfile.mySequenceIdLine == ELEVENTH_SEQID_LINE);
411 assert(fastqfile.mySequenceIdentifier == ELEVENTH_SEQID);
412 assert(fastqfile.myRawSequence == ELEVENTH_RAW_SEQ);
413 assert(fastqfile.myPlusLine == ELEVENTH_PLUS_LINE);
414 assert(fastqfile.myQualityString == ELEVENTH_QUALITY);
417 assert(fastqfile.mySequenceIdLine == TWELFTH_SEQID_LINE);
418 assert(fastqfile.mySequenceIdentifier == TWELFTH_SEQID);
419 assert(fastqfile.myRawSequence == TWELFTH_RAW_SEQ);
420 assert(fastqfile.myPlusLine == TWELFTH_PLUS_LINE);
421 assert(fastqfile.myQualityString == TWELFTH_QUALITY);
424 assert(fastqfile.mySequenceIdLine == THIRTEENTH_SEQID_LINE);
425 assert(fastqfile.mySequenceIdentifier == THIRTEENTH_SEQID);
426 assert(fastqfile.myRawSequence == THIRTEENTH_RAW_SEQ);
427 assert(fastqfile.myPlusLine == THIRTEENTH_PLUS_LINE);
428 assert(fastqfile.myQualityString == THIRTEENTH_QUALITY);
431 assert(fastqfile.mySequenceIdLine == FOURTEENTH_SEQID_LINE);
432 assert(fastqfile.mySequenceIdentifier == FOURTEENTH_SEQID);
433 assert(fastqfile.myRawSequence == FOURTEENTH_RAW_SEQ);
434 assert(fastqfile.myPlusLine == FOURTEENTH_PLUS_LINE);
435 assert(fastqfile.myQualityString == FOURTEENTH_QUALITY);
438 assert(fastqfile.mySequenceIdLine == FIFTEENTH_SEQID_LINE);
439 assert(fastqfile.mySequenceIdentifier == FIFTEENTH_SEQID);
440 assert(fastqfile.myRawSequence == FIFTEENTH_RAW_SEQ);
441 assert(fastqfile.myPlusLine == FIFTEENTH_PLUS_LINE);
442 assert(fastqfile.myQualityString == FIFTEENTH_QUALITY);
445 assert(fastqfile.mySequenceIdLine == SIXTEENTH_SEQID_LINE);
446 assert(fastqfile.mySequenceIdentifier == SIXTEENTH_SEQID);
447 assert(fastqfile.myRawSequence == SIXTEENTH_RAW_SEQ);
448 assert(fastqfile.myPlusLine == SIXTEENTH_PLUS_LINE);
449 assert(fastqfile.myQualityString == SIXTEENTH_QUALITY);
452 assert(fastqfile.mySequenceIdLine == SEVENTEENTH_SEQID_LINE);
453 assert(fastqfile.mySequenceIdentifier == SEVENTEENTH_SEQID);
454 assert(fastqfile.myRawSequence == SEVENTEENTH_RAW_SEQ);
455 assert(fastqfile.myPlusLine == SEVENTEENTH_PLUS_LINE);
456 assert(fastqfile.myQualityString == SEVENTEENTH_QUALITY);
459 assert(fastqfile.mySequenceIdLine == EIGHTEENTH_SEQID_LINE);
460 assert(fastqfile.mySequenceIdentifier == EIGHTEENTH_SEQID);
461 assert(fastqfile.myRawSequence == EIGHTEENTH_RAW_SEQ);
462 assert(fastqfile.myPlusLine == EIGHTEENTH_PLUS_LINE);
463 assert(fastqfile.myQualityString == EIGHTEENTH_QUALITY);
466 assert(fastqfile.mySequenceIdLine == NINETEENTH_SEQID_LINE);
467 assert(fastqfile.mySequenceIdentifier == NINETEENTH_SEQID);
468 assert(fastqfile.myRawSequence == NINETEENTH_RAW_SEQ);
469 assert(fastqfile.myPlusLine == NINETEENTH_PLUS_LINE);
470 assert(fastqfile.myQualityString == NINETEENTH_QUALITY);
473 assert(fastqfile.mySequenceIdLine == TWENTIETH_SEQID_LINE);
474 assert(fastqfile.mySequenceIdentifier == TWENTIETH_SEQID);
475 assert(fastqfile.myRawSequence == TWENTIETH_RAW_SEQ);
476 assert(fastqfile.myPlusLine == TWENTIETH_PLUS_LINE);
477 assert(fastqfile.myQualityString == TWENTIETH_QUALITY);
480 assert(fastqfile.mySequenceIdLine == TWENTY_FIRST_SEQID_LINE);
481 assert(fastqfile.mySequenceIdentifier == TWENTY_FIRST_SEQID);
482 assert(fastqfile.myRawSequence == TWENTY_FIRST_RAW_SEQ);
483 assert(fastqfile.myPlusLine == TWENTY_FIRST_PLUS_LINE);
484 assert(fastqfile.myQualityString == TWENTY_FIRST_QUALITY);
488 assert(fastqfile.
isOpen() ==
false);
493 assert(fastqfile.
isOpen() ==
false);
496 assert(fastqfile.
isOpen() ==
true);
502 assert(fastqfile.mySequenceIdLine == FIRST_SEQID_LINE);
503 assert(fastqfile.mySequenceIdentifier == FIRST_SEQID);
504 assert(fastqfile.myRawSequence == FIRST_RAW_SEQ);
505 assert(fastqfile.myPlusLine == FIRST_PLUS_LINE);
506 assert(fastqfile.myQualityString == FIRST_QUALITY);
510 assert(fastqfile.mySequenceIdLine == SECOND_SEQID_LINE);
511 assert(fastqfile.mySequenceIdentifier == SECOND_SEQID);
512 assert(fastqfile.myRawSequence == SECOND_RAW_SEQ);
513 assert(fastqfile.myPlusLine == SECOND_PLUS_LINE);
514 assert(fastqfile.myQualityString == SECOND_QUALITY);
517 assert(fastqfile.mySequenceIdLine == THIRD_SEQID_LINE);
518 assert(fastqfile.mySequenceIdentifier == THIRD_SEQID);
519 assert(fastqfile.myRawSequence == THIRD_RAW_SEQ);
520 assert(fastqfile.myPlusLine == THIRD_PLUS_LINE);
521 assert(fastqfile.myQualityString == THIRD_QUALITY);
524 assert(fastqfile.mySequenceIdLine == FOURTH_SEQID_LINE);
525 assert(fastqfile.mySequenceIdentifier == FOURTH_SEQID);
526 assert(fastqfile.myRawSequence == FOURTH_RAW_SEQ);
527 assert(fastqfile.myPlusLine == FOURTH_PLUS_LINE);
528 assert(fastqfile.myQualityString == FOURTH_QUALITY);
531 assert(fastqfile.mySequenceIdLine == FIFTH_SEQID_LINE);
532 assert(fastqfile.mySequenceIdentifier == FIFTH_SEQID);
533 assert(fastqfile.myRawSequence == FIFTH_RAW_SEQ);
534 assert(fastqfile.myPlusLine == FIFTH_PLUS_LINE);
535 assert(fastqfile.myQualityString == FIFTH_QUALITY);
538 assert(fastqfile.mySequenceIdLine == SIXTH_SEQID_LINE);
539 assert(fastqfile.mySequenceIdentifier == SIXTH_SEQID);
540 assert(fastqfile.myRawSequence == SIXTH_RAW_SEQ);
541 assert(fastqfile.myPlusLine == SIXTH_PLUS_LINE);
542 assert(fastqfile.myQualityString == SIXTH_QUALITY);
545 assert(fastqfile.mySequenceIdLine == SEVENTH_SEQID_LINE);
546 assert(fastqfile.mySequenceIdentifier == SEVENTH_SEQID);
547 assert(fastqfile.myRawSequence == SEVENTH_RAW_SEQ);
548 assert(fastqfile.myPlusLine == SEVENTH_PLUS_LINE);
549 assert(fastqfile.myQualityString == SEVENTH_QUALITY);
552 assert(fastqfile.mySequenceIdLine == EIGHTH_SEQID_LINE);
553 assert(fastqfile.mySequenceIdentifier == EIGHTH_SEQID);
554 assert(fastqfile.myRawSequence == EIGHTH_RAW_SEQ);
555 assert(fastqfile.myPlusLine == EIGHTH_PLUS_LINE);
556 assert(fastqfile.myQualityString == EIGHTH_QUALITY);
559 assert(fastqfile.mySequenceIdLine == NINTH_SEQID_LINE);
560 assert(fastqfile.mySequenceIdentifier == NINTH_SEQID);
561 assert(fastqfile.myRawSequence == NINTH_RAW_SEQ);
562 assert(fastqfile.myPlusLine == NINTH_PLUS_LINE);
563 assert(fastqfile.myQualityString == NINTH_QUALITY);
566 assert(fastqfile.mySequenceIdLine == TENTH_SEQID_LINE);
567 assert(fastqfile.mySequenceIdentifier == TENTH_SEQID);
568 assert(fastqfile.myRawSequence == TENTH_RAW_SEQ);
569 assert(fastqfile.myPlusLine == TENTH_PLUS_LINE);
570 assert(fastqfile.myQualityString == TENTH_QUALITY);
573 assert(fastqfile.mySequenceIdLine == ELEVENTH_SEQID_LINE);
574 assert(fastqfile.mySequenceIdentifier == ELEVENTH_SEQID);
575 assert(fastqfile.myRawSequence == ELEVENTH_RAW_SEQ);
576 assert(fastqfile.myPlusLine == ELEVENTH_PLUS_LINE);
577 assert(fastqfile.myQualityString == ELEVENTH_QUALITY);
580 assert(fastqfile.mySequenceIdLine == TWELFTH_SEQID_LINE);
581 assert(fastqfile.mySequenceIdentifier == TWELFTH_SEQID);
582 assert(fastqfile.myRawSequence == TWELFTH_RAW_SEQ);
583 assert(fastqfile.myPlusLine == TWELFTH_PLUS_LINE);
584 assert(fastqfile.myQualityString == TWELFTH_QUALITY);
587 assert(fastqfile.mySequenceIdLine == THIRTEENTH_SEQID_LINE);
588 assert(fastqfile.mySequenceIdentifier == THIRTEENTH_SEQID);
589 assert(fastqfile.myRawSequence == THIRTEENTH_RAW_SEQ);
590 assert(fastqfile.myPlusLine == THIRTEENTH_PLUS_LINE);
591 assert(fastqfile.myQualityString == THIRTEENTH_QUALITY);
594 assert(fastqfile.mySequenceIdLine == FOURTEENTH_SEQID_LINE);
595 assert(fastqfile.mySequenceIdentifier == FOURTEENTH_SEQID);
596 assert(fastqfile.myRawSequence == FOURTEENTH_RAW_SEQ);
597 assert(fastqfile.myPlusLine == FOURTEENTH_PLUS_LINE);
598 assert(fastqfile.myQualityString == FOURTEENTH_QUALITY);
601 assert(fastqfile.mySequenceIdLine == FIFTEENTH_SEQID_LINE);
602 assert(fastqfile.mySequenceIdentifier == FIFTEENTH_SEQID);
603 assert(fastqfile.myRawSequence == FIFTEENTH_RAW_SEQ);
604 assert(fastqfile.myPlusLine == FIFTEENTH_PLUS_LINE);
605 assert(fastqfile.myQualityString == FIFTEENTH_QUALITY);
608 assert(fastqfile.mySequenceIdLine == SIXTEENTH_SEQID_LINE);
609 assert(fastqfile.mySequenceIdentifier == SIXTEENTH_SEQID);
610 assert(fastqfile.myRawSequence == SIXTEENTH_RAW_SEQ);
611 assert(fastqfile.myPlusLine == SIXTEENTH_PLUS_LINE);
612 assert(fastqfile.myQualityString == SIXTEENTH_QUALITY);
615 assert(fastqfile.mySequenceIdLine == SEVENTEENTH_SEQID_LINE);
616 assert(fastqfile.mySequenceIdentifier == SEVENTEENTH_SEQID);
617 assert(fastqfile.myRawSequence == SEVENTEENTH_RAW_SEQ);
618 assert(fastqfile.myPlusLine == SEVENTEENTH_PLUS_LINE);
619 assert(fastqfile.myQualityString == SEVENTEENTH_QUALITY);
622 assert(fastqfile.mySequenceIdLine == EIGHTEENTH_SEQID_LINE);
623 assert(fastqfile.mySequenceIdentifier == EIGHTEENTH_SEQID);
624 assert(fastqfile.myRawSequence == EIGHTEENTH_RAW_SEQ);
625 assert(fastqfile.myPlusLine == EIGHTEENTH_PLUS_LINE);
626 assert(fastqfile.myQualityString == EIGHTEENTH_QUALITY);
629 assert(fastqfile.mySequenceIdLine == NINETEENTH_SEQID_LINE);
630 assert(fastqfile.mySequenceIdentifier == NINETEENTH_SEQID);
631 assert(fastqfile.myRawSequence == NINETEENTH_RAW_SEQ);
632 assert(fastqfile.myPlusLine == NINETEENTH_PLUS_LINE);
633 assert(fastqfile.myQualityString == NINETEENTH_QUALITY);
636 assert(fastqfile.mySequenceIdLine == TWENTIETH_SEQID_LINE);
637 assert(fastqfile.mySequenceIdentifier == TWENTIETH_SEQID);
638 assert(fastqfile.myRawSequence == TWENTIETH_RAW_SEQ);
639 assert(fastqfile.myPlusLine == TWENTIETH_PLUS_LINE);
640 assert(fastqfile.myQualityString == TWENTIETH_QUALITY);
643 assert(fastqfile.mySequenceIdLine == TWENTY_FIRST_SEQID_LINE);
644 assert(fastqfile.mySequenceIdentifier == TWENTY_FIRST_SEQID);
645 assert(fastqfile.myRawSequence == TWENTY_FIRST_RAW_SEQ);
646 assert(fastqfile.myPlusLine == TWENTY_FIRST_PLUS_LINE);
647 assert(fastqfile.myQualityString == TWENTY_FIRST_QUALITY);
651 assert(fastqfile.
isOpen() ==
false);
655 assert(fastqfile.
isOpen() ==
false);
658 assert(fastqfile.
isOpen() ==
true);
664 assert(fastqfile.mySequenceIdLine == FIRST_SEQID_LINE);
665 assert(fastqfile.mySequenceIdentifier == FIRST_SEQID);
666 assert(fastqfile.myRawSequence == FIRST_RAW_SEQ);
667 assert(fastqfile.myPlusLine == FIRST_PLUS_LINE);
668 assert(fastqfile.myQualityString == FIRST_QUALITY);
672 assert(fastqfile.mySequenceIdLine == SECOND_SEQID_LINE);
673 assert(fastqfile.mySequenceIdentifier == SECOND_SEQID);
674 assert(fastqfile.myRawSequence == SECOND_RAW_SEQ);
675 assert(fastqfile.myPlusLine == SECOND_PLUS_LINE);
676 assert(fastqfile.myQualityString == SECOND_QUALITY);
679 assert(fastqfile.mySequenceIdLine == THIRD_SEQID_LINE);
680 assert(fastqfile.mySequenceIdentifier == THIRD_SEQID);
681 assert(fastqfile.myRawSequence == THIRD_RAW_SEQ);
682 assert(fastqfile.myPlusLine == THIRD_PLUS_LINE);
683 assert(fastqfile.myQualityString == THIRD_QUALITY);
686 assert(fastqfile.mySequenceIdLine == FOURTH_SEQID_LINE);
687 assert(fastqfile.mySequenceIdentifier == FOURTH_SEQID);
688 assert(fastqfile.myRawSequence == FOURTH_RAW_SEQ);
689 assert(fastqfile.myPlusLine == FOURTH_PLUS_LINE);
690 assert(fastqfile.myQualityString == FOURTH_QUALITY);
693 assert(fastqfile.mySequenceIdLine == FIFTH_SEQID_LINE);
694 assert(fastqfile.mySequenceIdentifier == FIFTH_SEQID);
695 assert(fastqfile.myRawSequence == FIFTH_RAW_SEQ);
696 assert(fastqfile.myPlusLine == FIFTH_PLUS_LINE);
697 assert(fastqfile.myQualityString == FIFTH_QUALITY);
700 assert(fastqfile.mySequenceIdLine == SIXTH_SEQID_LINE);
701 assert(fastqfile.mySequenceIdentifier == SIXTH_SEQID);
702 assert(fastqfile.myRawSequence == SIXTH_RAW_SEQ);
703 assert(fastqfile.myPlusLine == SIXTH_PLUS_LINE);
704 assert(fastqfile.myQualityString == SIXTH_QUALITY);
707 assert(fastqfile.mySequenceIdLine == SEVENTH_SEQID_LINE);
708 assert(fastqfile.mySequenceIdentifier == SEVENTH_SEQID);
709 assert(fastqfile.myRawSequence == SEVENTH_RAW_SEQ);
710 assert(fastqfile.myPlusLine == SEVENTH_PLUS_LINE);
711 assert(fastqfile.myQualityString == SEVENTH_QUALITY);
714 assert(fastqfile.mySequenceIdLine == EIGHTH_SEQID_LINE);
715 assert(fastqfile.mySequenceIdentifier == EIGHTH_SEQID);
716 assert(fastqfile.myRawSequence == EIGHTH_RAW_SEQ);
717 assert(fastqfile.myPlusLine == EIGHTH_PLUS_LINE);
718 assert(fastqfile.myQualityString == EIGHTH_QUALITY);
721 assert(fastqfile.mySequenceIdLine == NINTH_SEQID_LINE);
722 assert(fastqfile.mySequenceIdentifier == NINTH_SEQID);
723 assert(fastqfile.myRawSequence == NINTH_RAW_SEQ);
724 assert(fastqfile.myPlusLine == NINTH_PLUS_LINE);
725 assert(fastqfile.myQualityString == NINTH_QUALITY);
728 assert(fastqfile.mySequenceIdLine == TENTH_SEQID_LINE);
729 assert(fastqfile.mySequenceIdentifier == TENTH_SEQID);
730 assert(fastqfile.myRawSequence == TENTH_RAW_SEQ);
731 assert(fastqfile.myPlusLine == TENTH_PLUS_LINE);
732 assert(fastqfile.myQualityString == TENTH_QUALITY);
735 assert(fastqfile.mySequenceIdLine == ELEVENTH_SEQID_LINE);
736 assert(fastqfile.mySequenceIdentifier == ELEVENTH_SEQID);
737 assert(fastqfile.myRawSequence == ELEVENTH_RAW_SEQ);
738 assert(fastqfile.myPlusLine == ELEVENTH_PLUS_LINE);
739 assert(fastqfile.myQualityString == ELEVENTH_QUALITY);
742 assert(fastqfile.mySequenceIdLine == TWELFTH_SEQID_LINE);
743 assert(fastqfile.mySequenceIdentifier == TWELFTH_SEQID);
744 assert(fastqfile.myRawSequence == TWELFTH_RAW_SEQ);
745 assert(fastqfile.myPlusLine == TWELFTH_PLUS_LINE);
746 assert(fastqfile.myQualityString == TWELFTH_QUALITY);
749 assert(fastqfile.mySequenceIdLine == THIRTEENTH_SEQID_LINE);
750 assert(fastqfile.mySequenceIdentifier == THIRTEENTH_SEQID);
751 assert(fastqfile.myRawSequence == THIRTEENTH_RAW_SEQ);
752 assert(fastqfile.myPlusLine == THIRTEENTH_PLUS_LINE);
753 assert(fastqfile.myQualityString == THIRTEENTH_QUALITY);
756 assert(fastqfile.mySequenceIdLine == FOURTEENTH_SEQID_LINE);
757 assert(fastqfile.mySequenceIdentifier == FOURTEENTH_SEQID);
758 assert(fastqfile.myRawSequence == FOURTEENTH_RAW_SEQ);
759 assert(fastqfile.myPlusLine == FOURTEENTH_PLUS_LINE);
760 assert(fastqfile.myQualityString == FOURTEENTH_QUALITY);
763 assert(fastqfile.mySequenceIdLine == FIFTEENTH_SEQID_LINE);
764 assert(fastqfile.mySequenceIdentifier == FIFTEENTH_SEQID);
765 assert(fastqfile.myRawSequence == FIFTEENTH_RAW_SEQ);
766 assert(fastqfile.myPlusLine == FIFTEENTH_PLUS_LINE);
767 assert(fastqfile.myQualityString == FIFTEENTH_QUALITY);
770 assert(fastqfile.mySequenceIdLine == SIXTEENTH_SEQID_LINE);
771 assert(fastqfile.mySequenceIdentifier == SIXTEENTH_SEQID);
772 assert(fastqfile.myRawSequence == SIXTEENTH_RAW_SEQ);
773 assert(fastqfile.myPlusLine == SIXTEENTH_PLUS_LINE);
774 assert(fastqfile.myQualityString == SIXTEENTH_QUALITY);
777 assert(fastqfile.mySequenceIdLine == SEVENTEENTH_SEQID_LINE);
778 assert(fastqfile.mySequenceIdentifier == SEVENTEENTH_SEQID);
779 assert(fastqfile.myRawSequence == SEVENTEENTH_RAW_SEQ);
780 assert(fastqfile.myPlusLine == SEVENTEENTH_PLUS_LINE);
781 assert(fastqfile.myQualityString == SEVENTEENTH_QUALITY);
784 assert(fastqfile.mySequenceIdLine == EIGHTEENTH_SEQID_LINE);
785 assert(fastqfile.mySequenceIdentifier == EIGHTEENTH_SEQID);
786 assert(fastqfile.myRawSequence == EIGHTEENTH_RAW_SEQ);
787 assert(fastqfile.myPlusLine == EIGHTEENTH_PLUS_LINE);
788 assert(fastqfile.myQualityString == EIGHTEENTH_QUALITY);
791 assert(fastqfile.mySequenceIdLine == NINETEENTH_SEQID_LINE);
792 assert(fastqfile.mySequenceIdentifier == NINETEENTH_SEQID);
793 assert(fastqfile.myRawSequence == NINETEENTH_RAW_SEQ);
794 assert(fastqfile.myPlusLine == NINETEENTH_PLUS_LINE);
795 assert(fastqfile.myQualityString == NINETEENTH_QUALITY);
798 assert(fastqfile.mySequenceIdLine == TWENTIETH_SEQID_LINE);
799 assert(fastqfile.mySequenceIdentifier == TWENTIETH_SEQID);
800 assert(fastqfile.myRawSequence == TWENTIETH_RAW_SEQ);
801 assert(fastqfile.myPlusLine == TWENTIETH_PLUS_LINE);
802 assert(fastqfile.myQualityString == TWENTIETH_QUALITY);
805 assert(fastqfile.mySequenceIdLine == TWENTY_FIRST_SEQID_LINE);
806 assert(fastqfile.mySequenceIdentifier == TWENTY_FIRST_SEQID);
807 assert(fastqfile.myRawSequence == TWENTY_FIRST_RAW_SEQ);
808 assert(fastqfile.myPlusLine == TWENTY_FIRST_PLUS_LINE);
809 assert(fastqfile.myQualityString == TWENTY_FIRST_QUALITY);
813 assert(fastqfile.
isOpen() ==
false);
819 assert(fastqfile.
isOpen() ==
false);
822 assert(fastqfile.
isOpen() ==
true);
828 assert(fastqfile.mySequenceIdLine == FIRST_SEQID_LINE);
829 assert(fastqfile.mySequenceIdentifier == FIRST_SEQID);
830 assert(fastqfile.myRawSequence == FIRST_RAW_SEQ);
831 assert(fastqfile.myPlusLine == FIRST_PLUS_LINE);
832 assert(fastqfile.myQualityString == FIRST_QUALITY);
836 assert(fastqfile.mySequenceIdLine == SECOND_SEQID_LINE);
837 assert(fastqfile.mySequenceIdentifier == SECOND_SEQID);
838 assert(fastqfile.myRawSequence == SECOND_RAW_SEQ);
839 assert(fastqfile.myPlusLine == SECOND_PLUS_LINE);
840 assert(fastqfile.myQualityString == SECOND_QUALITY);
843 assert(fastqfile.mySequenceIdLine == THIRD_SEQID_LINE);
844 assert(fastqfile.mySequenceIdentifier == THIRD_SEQID);
845 assert(fastqfile.myRawSequence == THIRD_RAW_SEQ);
846 assert(fastqfile.myPlusLine == THIRD_PLUS_LINE);
847 assert(fastqfile.myQualityString == THIRD_QUALITY);
850 assert(fastqfile.mySequenceIdLine == FOURTH_SEQID_LINE);
851 assert(fastqfile.mySequenceIdentifier == FOURTH_SEQID);
852 assert(fastqfile.myRawSequence == FOURTH_RAW_SEQ);
853 assert(fastqfile.myPlusLine == FOURTH_PLUS_LINE);
854 assert(fastqfile.myQualityString == FOURTH_QUALITY);
857 assert(fastqfile.mySequenceIdLine == FIFTH_SEQID_LINE);
858 assert(fastqfile.mySequenceIdentifier == FIFTH_SEQID);
859 assert(fastqfile.myRawSequence == FIFTH_RAW_SEQ);
860 assert(fastqfile.myPlusLine == FIFTH_PLUS_LINE);
861 assert(fastqfile.myQualityString == FIFTH_QUALITY);
864 assert(fastqfile.mySequenceIdLine == SIXTH_SEQID_LINE);
865 assert(fastqfile.mySequenceIdentifier == SIXTH_SEQID);
866 assert(fastqfile.myRawSequence == SIXTH_RAW_SEQ);
867 assert(fastqfile.myPlusLine == SIXTH_PLUS_LINE);
868 assert(fastqfile.myQualityString == SIXTH_QUALITY);
871 assert(fastqfile.mySequenceIdLine == SEVENTH_SEQID_LINE);
872 assert(fastqfile.mySequenceIdentifier == SEVENTH_SEQID);
873 assert(fastqfile.myRawSequence == SEVENTH_RAW_SEQ);
874 assert(fastqfile.myPlusLine == SEVENTH_PLUS_LINE);
875 assert(fastqfile.myQualityString == SEVENTH_QUALITY);
878 assert(fastqfile.mySequenceIdLine == EIGHTH_SEQID_LINE);
879 assert(fastqfile.mySequenceIdentifier == EIGHTH_SEQID);
880 assert(fastqfile.myRawSequence == EIGHTH_RAW_SEQ);
881 assert(fastqfile.myPlusLine == EIGHTH_PLUS_LINE);
882 assert(fastqfile.myQualityString == EIGHTH_QUALITY);
885 assert(fastqfile.mySequenceIdLine == NINTH_SEQID_LINE);
886 assert(fastqfile.mySequenceIdentifier == NINTH_SEQID);
887 assert(fastqfile.myRawSequence == NINTH_RAW_SEQ);
888 assert(fastqfile.myPlusLine == NINTH_PLUS_LINE);
889 assert(fastqfile.myQualityString == NINTH_QUALITY);
892 assert(fastqfile.mySequenceIdLine == TENTH_SEQID_LINE);
893 assert(fastqfile.mySequenceIdentifier == TENTH_SEQID);
894 assert(fastqfile.myRawSequence == TENTH_RAW_SEQ);
895 assert(fastqfile.myPlusLine == TENTH_PLUS_LINE);
896 assert(fastqfile.myQualityString == TENTH_QUALITY);
899 assert(fastqfile.mySequenceIdLine == ELEVENTH_SEQID_LINE);
900 assert(fastqfile.mySequenceIdentifier == ELEVENTH_SEQID);
901 assert(fastqfile.myRawSequence == ELEVENTH_RAW_SEQ);
902 assert(fastqfile.myPlusLine == ELEVENTH_PLUS_LINE);
903 assert(fastqfile.myQualityString == ELEVENTH_QUALITY);
906 assert(fastqfile.mySequenceIdLine == TWELFTH_SEQID_LINE);
907 assert(fastqfile.mySequenceIdentifier == TWELFTH_SEQID);
908 assert(fastqfile.myRawSequence == TWELFTH_RAW_SEQ);
909 assert(fastqfile.myPlusLine == TWELFTH_PLUS_LINE);
910 assert(fastqfile.myQualityString == TWELFTH_QUALITY);
913 assert(fastqfile.mySequenceIdLine == THIRTEENTH_SEQID_LINE);
914 assert(fastqfile.mySequenceIdentifier == THIRTEENTH_SEQID);
915 assert(fastqfile.myRawSequence == THIRTEENTH_RAW_SEQ);
916 assert(fastqfile.myPlusLine == THIRTEENTH_PLUS_LINE);
917 assert(fastqfile.myQualityString == THIRTEENTH_QUALITY);
920 assert(fastqfile.mySequenceIdLine == FOURTEENTH_SEQID_LINE);
921 assert(fastqfile.mySequenceIdentifier == FOURTEENTH_SEQID);
922 assert(fastqfile.myRawSequence == FOURTEENTH_RAW_SEQ);
923 assert(fastqfile.myPlusLine == FOURTEENTH_PLUS_LINE);
924 assert(fastqfile.myQualityString == FOURTEENTH_QUALITY);
927 assert(fastqfile.mySequenceIdLine == FIFTEENTH_SEQID_LINE);
928 assert(fastqfile.mySequenceIdentifier == FIFTEENTH_SEQID);
929 assert(fastqfile.myRawSequence == FIFTEENTH_RAW_SEQ);
930 assert(fastqfile.myPlusLine == FIFTEENTH_PLUS_LINE);
931 assert(fastqfile.myQualityString == FIFTEENTH_QUALITY);
934 assert(fastqfile.mySequenceIdLine == SIXTEENTH_SEQID_LINE);
935 assert(fastqfile.mySequenceIdentifier == SIXTEENTH_SEQID);
936 assert(fastqfile.myRawSequence == SIXTEENTH_RAW_SEQ);
937 assert(fastqfile.myPlusLine == SIXTEENTH_PLUS_LINE);
938 assert(fastqfile.myQualityString == SIXTEENTH_QUALITY);
941 assert(fastqfile.mySequenceIdLine == SEVENTEENTH_SEQID_LINE);
942 assert(fastqfile.mySequenceIdentifier == SEVENTEENTH_SEQID);
943 assert(fastqfile.myRawSequence == SEVENTEENTH_RAW_SEQ);
944 assert(fastqfile.myPlusLine == SEVENTEENTH_PLUS_LINE);
945 assert(fastqfile.myQualityString == SEVENTEENTH_QUALITY);
948 assert(fastqfile.mySequenceIdLine == EIGHTEENTH_SEQID_LINE);
949 assert(fastqfile.mySequenceIdentifier == EIGHTEENTH_SEQID);
950 assert(fastqfile.myRawSequence == EIGHTEENTH_RAW_SEQ);
951 assert(fastqfile.myPlusLine == EIGHTEENTH_PLUS_LINE);
952 assert(fastqfile.myQualityString == EIGHTEENTH_QUALITY);
955 assert(fastqfile.mySequenceIdLine == NINETEENTH_SEQID_LINE);
956 assert(fastqfile.mySequenceIdentifier == NINETEENTH_SEQID);
957 assert(fastqfile.myRawSequence == NINETEENTH_RAW_SEQ);
958 assert(fastqfile.myPlusLine == NINETEENTH_PLUS_LINE);
959 assert(fastqfile.myQualityString == NINETEENTH_QUALITY);
962 assert(fastqfile.mySequenceIdLine == TWENTIETH_SEQID_LINE);
963 assert(fastqfile.mySequenceIdentifier == TWENTIETH_SEQID);
964 assert(fastqfile.myRawSequence == TWENTIETH_RAW_SEQ);
965 assert(fastqfile.myPlusLine == TWENTIETH_PLUS_LINE);
966 assert(fastqfile.myQualityString == TWENTIETH_QUALITY);
969 assert(fastqfile.mySequenceIdLine == TWENTY_FIRST_SEQID_LINE);
970 assert(fastqfile.mySequenceIdentifier == TWENTY_FIRST_SEQID);
971 assert(fastqfile.myRawSequence == TWENTY_FIRST_RAW_SEQ);
972 assert(fastqfile.myPlusLine == TWENTY_FIRST_PLUS_LINE);
973 assert(fastqfile.myQualityString == TWENTY_FIRST_QUALITY);
977 assert(fastqfile.
isOpen() ==
false);
982int main(
int argc,
char ** argv)
984 testReadUnOpenedFile();
@ COLOR_SPACE
Color space only (0,1,2,3,.).
@ UNKNOWN
Base decision on the first raw seq character/type has yet to be determined.
@ BASE_SPACE
Bases only (A,C,G,T,N).
Class for reading/validating a fastq file.
FastQStatus::Status openFile(const char *fileName, BaseAsciiMap::SPACE_TYPE spaceType=BaseAsciiMap::UNKNOWN)
Open a FastQFile.
bool isOpen()
Check to see if the file is open.
void disableSeqIDCheck()
Disable Unique Sequence ID checking (Unique Sequence ID checking is enabled by default).
BaseAsciiMap::SPACE_TYPE getSpaceType()
Get the space type used for this file.
FastQStatus::Status readFastQSequence()
Read 1 FastQSequence, validating it.
FastQStatus::Status closeFile()
Close a FastQFile.
@ FASTQ_ORDER_ERROR
means the methods are called out of order, like trying to read a file before opening it.
@ FASTQ_SUCCESS
indicates method finished successfully.
@ FASTQ_INVALID
means that the sequence was invalid.
@ FASTQ_OPEN_ERROR
means the file could not be opened.