96 			BBIndex.setFractionToExclude(BBIndex.FRACTION_GENOME_TO_EXCLUDE*1.25f);  in preparse()
112 			BBIndex.setFractionToExclude(0);  in preparse()
137 			BBIndex.setFractionToExclude(BBIndex.FRACTION_GENOME_TO_EXCLUDE*0.4f);  in preparse()
149 			BBIndex.setFractionToExclude(excludeFraction);  in preparse()
164 			BBIndex.MAX_INDEL=maxIndel1;  in postparse()
167 			BBIndex.MAX_INDEL2=maxIndel2;  in postparse()
171 			BBIndex.MIN_APPROX_HITS_TO_KEEP=minApproxHits;  in postparse()
180 			BBIndex.setFractionToExclude(fractionGenomeToExclude);  in postparse()
196 			BBIndex.MAX_INDEL=Tools.min(BBIndex.MAX_INDEL, halfwidth/2);  in postparse()
197 			BBIndex.MAX_INDEL2=Tools.min(BBIndex.MAX_INDEL2, halfwidth);  in postparse()
204 			BBIndex.QUIT_AFTER_TWO_PERFECTS=false;  in postparse()
210 				if(!PRINT_SECONDARY_ALIGNMENTS){BBIndex.QUIT_AFTER_TWO_PERFECTS=true;}  in postparse()
215 				BBIndex.QUIT_AFTER_TWO_PERFECTS=false;  in postparse()
221 				BBIndex.QUIT_AFTER_TWO_PERFECTS=false;  in postparse()
226 				BBIndex.QUIT_AFTER_TWO_PERFECTS=true;  in postparse()
289 			BBIndex.QUIT_AFTER_TWO_PERFECTS=false;  in processAmbig2()
293 			BBIndex.QUIT_AFTER_TWO_PERFECTS=false;  in processAmbig2()
296 			BBIndex.QUIT_AFTER_TWO_PERFECTS=true;  in processAmbig2()
300 			BBIndex.QUIT_AFTER_TWO_PERFECTS=false;  in processAmbig2()
304 			BBIndex.QUIT_AFTER_TWO_PERFECTS=false;  in processAmbig2()
329 				BBIndex.setChromBits(RefToIndex.chrombits);  in loadIndex()
371 		BBIndex.loadIndex(minChrom, maxChrom, keylen, !RefToIndex.NODISK, RefToIndex.NODISK);  in loadIndex()
376 				BBIndex.MAX_HITS_REDUCTION2+=1;  in loadIndex()
377 				BBIndex.MAXIMUM_MAX_HITS_REDUCTION+=1;  in loadIndex()
379 					BBIndex.setFractionToExclude(BBIndex.FRACTION_GENOME_TO_EXCLUDE*0.5f);  in loadIndex()
380 					BBIndex.MAXIMUM_MAX_HITS_REDUCTION+=1;  in loadIndex()
381 					BBIndex.HIT_REDUCTION_DIV=Tools.max(BBIndex.HIT_REDUCTION_DIV-1, 3);  in loadIndex()
383 					BBIndex.setFractionToExclude(BBIndex.FRACTION_GENOME_TO_EXCLUDE*0.6f);  in loadIndex()
385 					BBIndex.setFractionToExclude(BBIndex.FRACTION_GENOME_TO_EXCLUDE*0.75f);  in loadIndex()
420 		BBIndex.analyzeIndex(minChrom, maxChrom, BBIndex.FRACTION_GENOME_TO_EXCLUDE, keylen);  in loadIndex()
465 		if(paired){BBIndex.QUIT_AFTER_TWO_PERFECTS=false;}  in testSpeed()
535 			BBIndex.setSemiperfectMode();  in setSemiperfectMode()
549 			BBIndex.setPerfectMode();  in setPerfectMode()
557 		printSettings0(k, BBIndex.MAX_INDEL, MINIMUM_ALIGNMENT_SCORE_RATIO);  in printSettings()
563 			outstream.println("Block Subsections:     \t"+BBIndex.CHROMS_PER_BLOCK);  in printSettings()
564 … Remove:    \t"+String.format(Locale.ROOT, "%.4f", (BBIndex.REMOVE_FREQUENT_GENOME_FRACTION ? BBIn…  in printSettings()
566 			outstream.println("Hits To Keep:          \t"+BBIndex.MIN_APPROX_HITS_TO_KEEP);  in printSettings()
570 			outstream.println("Remove Clumpy:         \t"+BBIndex.REMOVE_CLUMPY);  in printSettings()
571 			if(BBIndex.REMOVE_CLUMPY){  in printSettings()
572 				outstream.println("CLUMPY_MAX_DIST:       \t"+BBIndex.CLUMPY_MAX_DIST);  in printSettings()
573 				outstream.println("CLUMPY_MIN_LENGTH:     \t"+BBIndex.CLUMPY_MIN_LENGTH_INDEX);  in printSettings()
574 				outstream.println("CLUMPY_FRACTION:       \t"+BBIndex.CLUMPY_FRACTION);  in printSettings()
576 			outstream.println("Remove Long Lists:     \t"+BBIndex.TRIM_LONG_HIT_LISTS);  in printSettings()
577 			if(BBIndex.TRIM_LONG_HIT_LISTS){  in printSettings()
578 				outstream.println("HIT_FRACTION_TO_RETAIN:\t"+BBIndex.HIT_FRACTION_TO_RETAIN);  in printSettings()
580 			outstream.println("Trim By Greedy:        \t"+BBIndex.TRIM_BY_GREEDY);  in printSettings()
581 			outstream.println("Trim By Total Sites:   \t"+BBIndex.TRIM_BY_TOTAL_SITE_COUNT);  in printSettings()
582 			if(BBIndex.TRIM_BY_TOTAL_SITE_COUNT){  in printSettings()
583 				outstream.println("MAX_AVG_SITES:         \t"+BBIndex.MAX_AVERAGE_LIST_TO_SEARCH);  in printSettings()
584 				outstream.println("MAX_AVG_SITES_2:       \t"+BBIndex.MAX_AVERAGE_LIST_TO_SEARCH2);  in printSettings()
585 				outstream.println("MAX_SHORTEST_SITE:     \t"+BBIndex.MAX_SHORTEST_LIST_TO_SEARCH);  in printSettings()
587 			outstream.println("Index Min Score:       \t"+BBIndex.MIN_SCORE_MULT);  in printSettings()
589 			outstream.println("Dynamic Trim:          \t"+BBIndex.DYNAMICALLY_TRIM_LOW_SCORES);  in printSettings()
590 			if(BBIndex.DYNAMICALLY_TRIM_LOW_SCORES){  in printSettings()
591 				outstream.println("DYNAMIC_SCORE_THRESH:  \t"+BBIndex.DYNAMIC_SCORE_THRESH);  in printSettings()