| /dports/biology/bbmap/bbmap/current/align2/ |
| H A D | MultiStateAligner10ts.java | 408 assert((time&TIMEMASK)==time); in fillLimitedX()
476 assert((time&TIMEMASK)==time); in fillLimitedX()
538 assert((time&TIMEMASK)==time); in fillLimitedX()
579 printMatrix(packed, rows, columns, TIMEMASK, SCOREOFFSET); in fillLimitedX() argument
883 assert((time&TIMEMASK)==time); in fillBanded1()
951 assert((time&TIMEMASK)==time); in fillBanded1()
1013 assert((time&TIMEMASK)==time); in fillBanded1()
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| H A D | MultiStateAligner9Flat.java | 400 assert((time&TIMEMASK)==time); in fillLimitedX()
468 assert((time&TIMEMASK)==time); in fillLimitedX()
530 assert((time&TIMEMASK)==time); in fillLimitedX()
571 printMatrix(packed, rows, columns, TIMEMASK, SCOREOFFSET); in fillLimitedX() argument
728 assert((time&TIMEMASK)==time); in fillUnlimited()
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| H A D | MultiStateAligner9PacBio.java | 400 assert((time&TIMEMASK)==time); in fillLimitedX()
468 assert((time&TIMEMASK)==time); in fillLimitedX()
530 assert((time&TIMEMASK)==time); in fillLimitedX()
571 printMatrix(packed, rows, columns, TIMEMASK, SCOREOFFSET); in fillLimitedX() argument
728 assert((time&TIMEMASK)==time); in fillUnlimited()
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| H A D | MultiStateAligner9XFlat.java | 398 assert((time&TIMEMASK)==time); in fillLimitedX()
463 assert((time&TIMEMASK)==time); in fillLimitedX()
524 assert((time&TIMEMASK)==time); in fillLimitedX()
565 printMatrix(packed, rows, columns, TIMEMASK, SCOREOFFSET); in fillLimitedX() argument
721 assert((time&TIMEMASK)==time); in fillUnlimited()
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| H A D | MultiStateAligner9ts.java | 391 assert((time&TIMEMASK)==time); in fillLimitedX()
459 assert((time&TIMEMASK)==time); in fillLimitedX()
521 assert((time&TIMEMASK)==time); in fillLimitedX()
708 assert((time&TIMEMASK)==time); in fillUnlimited()
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| H A D | MultiStateAligner11ts.java | 405 assert((time&TIMEMASK)==time); in fillLimitedX()
473 assert((time&TIMEMASK)==time); in fillLimitedX()
535 assert((time&TIMEMASK)==time); in fillLimitedX()
576 printMatrix(packed, rows, columns, TIMEMASK, SCOREOFFSET); in fillLimitedX() argument
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| H A D | MSA.java | 570 static void printMatrix(int[][][] packed, int readlen, int reflen, int TIMEMASK, int SCOREOFFSET){ in printMatrix()
576 …static void printMatrix(int[][][] packed, int readlen, int reflen, int TIMEMASK, int SCOREOFFSET, … in printMatrix()
589 public static final String toTimePacked(int[] a, int TIMEMASK, int lim){ in toTimePacked()
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| /dports/biology/bbmap/bbmap/current/aligner/ |
| H A D | MultiStateAligner9PacBioAdapter_WithBarriers.java | 381 assert((time&TIMEMASK)==time); in fillLimitedX()
449 assert((time&TIMEMASK)==time); in fillLimitedX()
511 assert((time&TIMEMASK)==time); in fillLimitedX()
699 assert((time&TIMEMASK)==time); in fillUnlimited()
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| H A D | MultiStateAligner9PacBioAdapter.java | 336 assert((time&TIMEMASK)==time); in fillLimitedX()
389 assert((time&TIMEMASK)==time); in fillLimitedX()
448 assert((time&TIMEMASK)==time); in fillLimitedX()
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| H A D | MultiStateAligner9PacBioAdapter2.java | 393 assert((time&TIMEMASK)==time); in fillLimitedX()
456 assert((time&TIMEMASK)==time); in fillLimitedX()
517 assert((time&TIMEMASK)==time); in fillLimitedX()
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| H A D | MultiStateAligner9PacBioAdapter3.java | 321 assert((time&TIMEMASK)==time); in fillLimitedX()
382 assert((time&TIMEMASK)==time); in fillLimitedX()
441 assert((time&TIMEMASK)==time); in fillLimitedX()
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| /dports/biology/bbmap/bbmap/jni/ |
| H A D | MultiStateAligner11tsJNI.c | 38 #define TIMEMASK (~((-1)<<TIMEBITS)) macro
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