| /dports/biology/seqan1/seqan-1.3.1/apps/splazers/ |
| H A D | outputFormat.h | 352 if(*ali_it1 != *ali_it0) in getCigarLine()
360 ++ali_it1; in getCigarLine()
367 ++ali_it1; in getCigarLine()
371 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
374 ++ali_it1; in getCigarLine()
393 ++ali_it1; in getCigarLine()
436 ++ali_it1; in getCigarLine()
443 ++ali_it1; in getCigarLine()
447 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
450 ++ali_it1; in getCigarLine()
[all …]
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| H A D | razers_spliced.h | 404 TAlignIterator ali_it1 = iter(row(align,1),0); in countErrorsInAlign() local
410 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in countErrorsInAlign()
412 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in countErrorsInAlign()
414 if(*ali_it1 != *ali_it0) in countErrorsInAlign()
417 ++ali_it1; in countErrorsInAlign()
422 ++ali_it1; in countErrorsInAlign()
425 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in countErrorsInAlign()
428 ++ali_it1; in countErrorsInAlign()
437 while(ali_it1 != ali_it1_stop) in countErrorsInAlign()
439 ++ali_it1; in countErrorsInAlign()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/splazers/ |
| H A D | outputFormat.h | 354 if(*ali_it1 != *ali_it0) in getCigarLine()
362 ++ali_it1; in getCigarLine()
369 ++ali_it1; in getCigarLine()
373 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
376 ++ali_it1; in getCigarLine()
395 ++ali_it1; in getCigarLine()
438 ++ali_it1; in getCigarLine()
445 ++ali_it1; in getCigarLine()
449 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
452 ++ali_it1; in getCigarLine()
[all …]
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| H A D | razers_spliced.h | 558 TAlignIterator ali_it1 = iter(row(align,1),0); in countErrorsInAlign() local
564 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in countErrorsInAlign()
566 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in countErrorsInAlign()
568 if(*ali_it1 != *ali_it0) in countErrorsInAlign()
571 ++ali_it1; in countErrorsInAlign()
576 ++ali_it1; in countErrorsInAlign()
579 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in countErrorsInAlign()
582 ++ali_it1; in countErrorsInAlign()
591 while(ali_it1 != ali_it1_stop) in countErrorsInAlign()
593 ++ali_it1; in countErrorsInAlign()
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| /dports/biology/seqan1/seqan-1.3.1/apps/razers/ |
| H A D | outputFormat.h | 344 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
349 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in getCigarLine()
352 if(*ali_it1 != *ali_it0) in getCigarLine()
360 ++ali_it1; in getCigarLine()
367 ++ali_it1; in getCigarLine()
371 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
374 ++ali_it1; in getCigarLine()
391 while(ali_it1 != ali_it1_stop) in getCigarLine()
393 ++ali_it1; in getCigarLine()
1154 TAlignIterator ali_it1 = iter(row(align,1),viewPosReadFirst); in dumpMatches() local
[all …]
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| H A D | razers_spliced.h | 392 TAlignIterator ali_it1 = iter(row(align,1),0); in countErrorsInAlign() local
398 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in countErrorsInAlign()
400 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in countErrorsInAlign()
402 if(*ali_it1 != *ali_it0) in countErrorsInAlign()
405 ++ali_it1; in countErrorsInAlign()
410 ++ali_it1; in countErrorsInAlign()
413 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in countErrorsInAlign()
416 ++ali_it1; in countErrorsInAlign()
425 while(ali_it1 != ali_it1_stop) in countErrorsInAlign()
427 ++ali_it1; in countErrorsInAlign()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers/ |
| H A D | outputFormat.h | 350 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
355 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in getCigarLine()
358 if(*ali_it1 != *ali_it0) in getCigarLine()
366 ++ali_it1; in getCigarLine()
373 ++ali_it1; in getCigarLine()
377 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
380 ++ali_it1; in getCigarLine()
397 while(ali_it1 != ali_it1_stop) in getCigarLine()
399 ++ali_it1; in getCigarLine()
1165 TAlignIterator ali_it1 = iter(row(align,1),viewPosReadFirst); in dumpMatches() local
[all …]
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| H A D | razers_spliced.h | 392 TAlignIterator ali_it1 = iter(row(align,1),0); in countErrorsInAlign() local
398 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in countErrorsInAlign()
400 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in countErrorsInAlign()
402 if(*ali_it1 != *ali_it0) in countErrorsInAlign()
405 ++ali_it1; in countErrorsInAlign()
410 ++ali_it1; in countErrorsInAlign()
413 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in countErrorsInAlign()
416 ++ali_it1; in countErrorsInAlign()
425 while(ali_it1 != ali_it1_stop) in countErrorsInAlign()
427 ++ali_it1; in countErrorsInAlign()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/ |
| H A D | casbar.h | 827 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1))
829 if(*ali_it1 != *ali_it0)
833 ++ali_it1;
839 ++ali_it1;
841 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop)
844 ++ali_it1;
869 …while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1) && refP…
874 ++ali_it1;
880 ++ali_it1;
882 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop && refPos <= pos_row1)
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| /dports/biology/seqan/seqan-library-2.4.0/include/seqan/align/ |
| H A D | local_alignment_waterman_eggert_impl.h | 350 TGapsVIter ali_it1 = end(gapsV); in _smithWatermanDeclump() local
409 if(ali_it0==ali_it0_stop && ali_it1==ali_it1_stop) in _smithWatermanDeclump()
422 --ali_it1; in _smithWatermanDeclump()
426 --ali_it1; in _smithWatermanDeclump()
428 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in _smithWatermanDeclump()
430 --ali_it1; in _smithWatermanDeclump()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/include/seqan/align/ |
| H A D | local_alignment_waterman_eggert_impl.h | 350 TGapsVIter ali_it1 = end(gapsV); in _smithWatermanDeclump() local
409 if(ali_it0==ali_it0_stop && ali_it1==ali_it1_stop) in _smithWatermanDeclump()
422 --ali_it1; in _smithWatermanDeclump()
426 --ali_it1; in _smithWatermanDeclump()
428 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in _smithWatermanDeclump()
430 --ali_it1; in _smithWatermanDeclump()
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| /dports/biology/pbseqan/seqan-21d95d737d8decb5cc3693b9065d81e831e7f57d/include/seqan/align/ |
| H A D | local_alignment_waterman_eggert_impl.h | 348 TGapsVIter ali_it1 = end(gapsV); in _smithWatermanDeclump() local
409 if(ali_it0==ali_it0_stop && ali_it1==ali_it1_stop) in _smithWatermanDeclump()
422 --ali_it1; in _smithWatermanDeclump()
426 --ali_it1; in _smithWatermanDeclump()
428 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in _smithWatermanDeclump()
430 --ali_it1; in _smithWatermanDeclump()
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| /dports/biology/seqan1/seqan-1.3.1/apps/snp_store/ |
| H A D | snp_store.h | 889 ++ali_it1;
895 ++ali_it1;
897 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop)
900 ++ali_it1;
930 ++ali_it1;
936 ++ali_it1;
942 ++ali_it1;
2537 ++ali_it1;
2543 ++ali_it1;
2551 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop)
[all …]
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| /dports/biology/seqan1/seqan-1.3.1/seqan/align/ |
| H A D | align_local_dynprog.h | 372 TAlignIterator ali_it1 = iter(row1,endPosition(row1)); in _smithWatermanDeclump() local
423 if(ali_it0==ali_it0_stop && ali_it1==ali_it1_stop) in _smithWatermanDeclump()
436 --ali_it1; in _smithWatermanDeclump()
440 --ali_it1; in _smithWatermanDeclump()
442 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in _smithWatermanDeclump()
444 --ali_it1; in _smithWatermanDeclump()
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| /dports/biology/seqan1/seqan-1.3.1/apps/razers2/ |
| H A D | outputFormat.h | 384 TAlignIterator ali_it1 = iter(row(align,1),beginPosition(cols(align))); in getCigarLine() local
389 while(ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
394 while(ali_it0!=ali_it0_stop && ali_it1!=ali_it1_stop && !isGap(ali_it0)&& !isGap(ali_it1)) in getCigarLine()
397 if(*ali_it1 != *ali_it0) in getCigarLine()
405 ++ali_it1; in getCigarLine()
412 ++ali_it1; in getCigarLine()
416 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop) in getCigarLine()
419 ++ali_it1; in getCigarLine()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/razers3/ |
| H A D | outputFormat.h | 410 TAlignIterator ali_it1 = iter(row(align, 1), beginPosition(cols(align))); in getCigarLine() local
415 while (ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop) in getCigarLine()
420 … while (ali_it0 != ali_it0_stop && ali_it1 != ali_it1_stop && !isGap(ali_it0) && !isGap(ali_it1)) in getCigarLine()
423 if (*ali_it1 != *ali_it0) in getCigarLine()
433 ++ali_it1; in getCigarLine()
441 ++ali_it1; in getCigarLine()
446 while (isGap(ali_it1) && ali_it1 != ali_it1_stop) in getCigarLine()
449 ++ali_it1; in getCigarLine()
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/snp_store/ |
| H A D | snp_store.h | 2235 ++ali_it1;
2241 ++ali_it1;
2243 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop)
2246 ++ali_it1;
2276 ++ali_it1;
2282 ++ali_it1;
2288 ++ali_it1;
4893 ++ali_it1;
4899 ++ali_it1;
4907 while(isGap(ali_it1)&& ali_it1!=ali_it1_stop)
[all …]
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