Lines Matching refs:found
24860 Genomecomp_T found, compare, flags; in block_find() local
24870 found = splicesite_bits[compare >> 16]; in block_find()
24871 *high_halfsite = (found & 0x100) >> 8; in block_find()
24872 found = (found << 24) | 0x00FFFFFF; in block_find()
24876 …found &= (splicesite_bits[compare & 0x0000FFFF] << 16) | 0xFE00FFFF; /* Use FE to allow for high b… in block_find()
24885 found &= (splicesite_bits[compare >> 16] << 8) | 0xFFFE00FF; in block_find()
24888 found &= splicesite_bits[compare & 0x0000FFFF] | 0xFFFFFE00; in block_find()
24890 splicesite_bits[compare & 0x0000FFFF],found & 0x1)); in block_find()
24901 found &= ~flags; in block_find()
24902 found &= ~(flags << 1); in block_find()
24904 *low_halfsite = found & 0x00000001; in block_find()
24910 found >>= 1; in block_find()
24911 …debug2(printf(" => found %08X, high_halfsite %d, low_halfsite %d\n",found,*high_halfsite,*low_half… in block_find()
24913 return found; in block_find()
24921 Genomecomp_T found, ref, alt, flags; in block_find_snp() local
24934 found = splicesite_bits[ref >> 16] | splicesite_bits[alt >> 16]; in block_find_snp()
24935 *high_halfsite = (found & 0x100) >> 8; in block_find_snp()
24936 found = (found << 24) | 0x00FFFFFF; in block_find_snp()
24941 …found &= ((splicesite_bits[ref & 0x0000FFFF] | splicesite_bits[alt & 0x0000FFFF]) << 16) | 0xFE00F… in block_find_snp()
24953 found &= ((splicesite_bits[ref >> 16] | splicesite_bits[alt >> 16]) << 8) | 0xFFFE00FF; in block_find_snp()
24957 found &= (splicesite_bits[ref & 0x0000FFFF] | splicesite_bits[alt & 0x0000FFFF]) | 0xFFFFFE00; in block_find_snp()
24959 splicesite_bits[ref & 0x0000FFFF],splicesite_bits[ref & 0x0000FFFF],found & 0x1)); in block_find_snp()
24971 found &= ~flags; in block_find_snp()
24972 found &= ~(flags << 1); in block_find_snp()
24974 *low_halfsite = found & 0x00000001; in block_find_snp()
24980 found >>= 1; in block_find_snp()
24981 …debug2(printf(" => found %08X, high_halfsite %d, low_halfsite %d\n",found,*high_halfsite,*low_half… in block_find_snp()
24983 return found; in block_find_snp()
24995 Genomecomp_T found; in splicesite_positions() local
25033 found = block_find_snp(&high_halfsite,&low_halfsite, in splicesite_positions()
25036 found = block_find(&high_halfsite,&low_halfsite,&(ref_blocks[startblocki]),splicesite_bits); in splicesite_positions()
25038 found = clear_start(found,startdiscard); in splicesite_positions()
25039 found = clear_end(found,enddiscard); in splicesite_positions()
25042 while (found != 0U) { in splicesite_positions()
25044 pos = offset + (relpos = __builtin_ctz(found)); in splicesite_positions()
25058 clear_lowbit(found,relpos); in splicesite_positions()
25060 debug2(printf("found is %08X, -found & found is %08X\n",found,-found & found)); in splicesite_positions()
25061 pos = offset + mod_37_bit_position[(lowbit = -found & found) % 37]; in splicesite_positions()
25075 found -= lowbit; in splicesite_positions()
25077 …debug2(printf("found is %08X => offset %llu + relpos %d\n",found,(unsigned long long) offset,relpo… in splicesite_positions()
25099 found = block_find_snp(&high_halfsite,&low_halfsite, in splicesite_positions()
25102 found = block_find(&high_halfsite,&low_halfsite,&(ref_blocks[startblocki]),splicesite_bits); in splicesite_positions()
25104 found = clear_start(found,startdiscard); in splicesite_positions()
25107 while (found != 0U) { in splicesite_positions()
25109 pos = offset + (relpos = __builtin_ctz(found)); in splicesite_positions()
25123 clear_lowbit(found,relpos); in splicesite_positions()
25125 debug2(printf("found is %08X, -found & found is %08X\n",found,-found & found)); in splicesite_positions()
25126 pos = offset + mod_37_bit_position[(lowbit = -found & found) % 37]; in splicesite_positions()
25140 found -= lowbit; in splicesite_positions()
25142 …debug2(printf("found is %08X => offset %llu + relpos %d\n",found,(unsigned long long) offset,relpo… in splicesite_positions()
25152 found = block_find_snp(&high_halfsite,&low_halfsite,ptr,altptr,splicesite_bits); in splicesite_positions()
25154 found = block_find(&high_halfsite,&low_halfsite,ptr,splicesite_bits); in splicesite_positions()
25175 while (found != 0U) { in splicesite_positions()
25177 pos = offset + (relpos = __builtin_ctz(found)); in splicesite_positions()
25191 clear_lowbit(found,relpos); in splicesite_positions()
25193 debug2(printf("found is %08X, -found & found is %08X\n",found,-found & found)); in splicesite_positions()
25194 pos = offset + mod_37_bit_position[(lowbit = -found & found) % 37]; in splicesite_positions()
25208 found -= lowbit; in splicesite_positions()
25210 …debug2(printf("found is %08X => offset %llu + relpos %d\n",found,(unsigned long long) offset,relpo… in splicesite_positions()
25221 found = block_find_snp(&high_halfsite,&low_halfsite,ptr,altptr,splicesite_bits); in splicesite_positions()
25223 found = block_find(&high_halfsite,&low_halfsite,ptr,splicesite_bits); in splicesite_positions()
25225 found = clear_end(found,enddiscard); in splicesite_positions()
25246 while (found != 0U) { in splicesite_positions()
25248 pos = offset + (relpos = __builtin_ctz(found)); in splicesite_positions()
25262 clear_lowbit(found,relpos); in splicesite_positions()
25264 debug2(printf("found is %08X, -found & found is %08X\n",found,-found & found)); in splicesite_positions()
25265 pos = offset + mod_37_bit_position[(lowbit = -found & found) % 37]; in splicesite_positions()
25279 found -= lowbit; in splicesite_positions()
25281 …debug2(printf("found is %08X => offset %llu + relpos %d\n",found,(unsigned long long) offset,relpo… in splicesite_positions()
25333 Genomecomp_T found; in splicesite_positions_novel() local
25364 found = block_find_snp(&high_halfsite,&low_halfsite, in splicesite_positions_novel()
25367 found = block_find(&high_halfsite,&low_halfsite,&(ref_blocks[startblocki]),splicesite_bits); in splicesite_positions_novel()
25369 found = clear_start(found,startdiscard); in splicesite_positions_novel()
25370 found = clear_end(found,enddiscard); in splicesite_positions_novel()
25373 while (found != 0U) { in splicesite_positions_novel()
25375 pos = offset + (relpos = __builtin_ctz(found)); in splicesite_positions_novel()
25377 clear_lowbit(found,relpos); in splicesite_positions_novel()
25379 debug2(printf("found is %08X, -found & found is %08X\n",found,-found & found)); in splicesite_positions_novel()
25380 pos = offset + mod_37_bit_position[(lowbit = -found & found) % 37]; in splicesite_positions_novel()
25382 found -= lowbit; in splicesite_positions_novel()
25384 …debug2(printf("found is %08X => offset %llu + relpos %d\n",found,(unsigned long long) offset,relpo… in splicesite_positions_novel()
25392 found = block_find_snp(&high_halfsite,&low_halfsite, in splicesite_positions_novel()
25395 found = block_find(&high_halfsite,&low_halfsite,&(ref_blocks[startblocki]),splicesite_bits); in splicesite_positions_novel()
25397 found = clear_start(found,startdiscard); in splicesite_positions_novel()
25400 while (found != 0U) { in splicesite_positions_novel()
25402 pos = offset + (relpos = __builtin_ctz(found)); in splicesite_positions_novel()
25404 clear_lowbit(found,relpos); in splicesite_positions_novel()
25406 debug2(printf("found is %08X, -found & found is %08X\n",found,-found & found)); in splicesite_positions_novel()
25407 pos = offset + mod_37_bit_position[(lowbit = -found & found) % 37]; in splicesite_positions_novel()
25409 found -= lowbit; in splicesite_positions_novel()
25411 …debug2(printf("found is %08X => offset %llu + relpos %d\n",found,(unsigned long long) offset,relpo… in splicesite_positions_novel()
25421 found = block_find_snp(&high_halfsite,&low_halfsite,ptr,altptr,splicesite_bits); in splicesite_positions_novel()
25423 found = block_find(&high_halfsite,&low_halfsite,ptr,splicesite_bits); in splicesite_positions_novel()
25432 while (found != 0U) { in splicesite_positions_novel()
25434 pos = offset + (relpos = __builtin_ctz(found)); in splicesite_positions_novel()
25436 clear_lowbit(found,relpos); in splicesite_positions_novel()
25438 debug2(printf("found is %08X, -found & found is %08X\n",found,-found & found)); in splicesite_positions_novel()
25439 pos = offset + mod_37_bit_position[(lowbit = -found & found) % 37]; in splicesite_positions_novel()
25441 found -= lowbit; in splicesite_positions_novel()
25443 …debug2(printf("found is %08X => offset %llu + relpos %d\n",found,(unsigned long long) offset,relpo… in splicesite_positions_novel()
25454 found = block_find_snp(&high_halfsite,&low_halfsite,ptr,altptr,splicesite_bits); in splicesite_positions_novel()
25456 found = block_find(&high_halfsite,&low_halfsite,ptr,splicesite_bits); in splicesite_positions_novel()
25458 found = clear_end(found,enddiscard); in splicesite_positions_novel()
25467 while (found != 0U) { in splicesite_positions_novel()
25469 pos = offset + (relpos = __builtin_ctz(found)); in splicesite_positions_novel()
25471 clear_lowbit(found,relpos); in splicesite_positions_novel()
25473 debug2(printf("found is %08X, -found & found is %08X\n",found,-found & found)); in splicesite_positions_novel()
25474 pos = offset + mod_37_bit_position[(lowbit = -found & found) % 37]; in splicesite_positions_novel()
25476 found -= lowbit; in splicesite_positions_novel()
25478 …debug2(printf("found is %08X => offset %llu + relpos %d\n",found,(unsigned long long) offset,relpo… in splicesite_positions_novel()
25523 Genomecomp_T found; in prev_dinucleotide_position() local
25546 found = block_find_snp(&high_halfsite,&low_halfsite, in prev_dinucleotide_position()
25549 found = block_find(&high_halfsite,&low_halfsite,&(ref_blocks[endblocki]),splicesite_bits); in prev_dinucleotide_position()
25551 found = clear_end(found,enddiscard); in prev_dinucleotide_position()
25553 found = clear_start(found,startdiscard); in prev_dinucleotide_position()
25555 if (found != 0U) { in prev_dinucleotide_position()
25557 foundpos = offset - (relpos = __builtin_clz(found)); in prev_dinucleotide_position()
25559 foundpos = offset - (relpos = (top = found >> 16) ? clz_table[top] : 16 + clz_table[found]); in prev_dinucleotide_position()
25562 found,(unsigned long long) offset,relpos,(unsigned long long) (foundpos-chroffset), in prev_dinucleotide_position()
25573 found = block_find_snp(&high_halfsite,&low_halfsite, in prev_dinucleotide_position()
25576 found = block_find(&high_halfsite,&low_halfsite,&(ref_blocks[endblocki]),splicesite_bits); in prev_dinucleotide_position()
25578 found = clear_end(found,enddiscard); in prev_dinucleotide_position()
25580 if (found != 0U) { in prev_dinucleotide_position()
25582 foundpos = offset - (relpos = __builtin_clz(found)); in prev_dinucleotide_position()
25584 foundpos = offset - (relpos = (top = found >> 16) ? clz_table[top] : 16 + clz_table[found]); in prev_dinucleotide_position()
25587 found,(unsigned long long) offset,relpos,(unsigned long long) (foundpos-chroffset), in prev_dinucleotide_position()
25601 found = block_find_snp(&high_halfsite,&low_halfsite,ptr,altptr,splicesite_bits); in prev_dinucleotide_position()
25603 found = block_find(&high_halfsite,&low_halfsite,ptr,splicesite_bits); in prev_dinucleotide_position()
25610 } else if (found != 0U) { in prev_dinucleotide_position()
25612 foundpos = offset - (relpos = __builtin_clz(found)); in prev_dinucleotide_position()
25614 foundpos = offset - (relpos = (top = found >> 16) ? clz_table[top] : 16 + clz_table[found]); in prev_dinucleotide_position()
25617 found,(unsigned long long) offset,relpos,(unsigned long long) (foundpos-chroffset), in prev_dinucleotide_position()
25630 found = block_find_snp(&high_halfsite,&low_halfsite,ptr,altptr,splicesite_bits); in prev_dinucleotide_position()
25632 found = block_find(&high_halfsite,&low_halfsite,ptr,splicesite_bits); in prev_dinucleotide_position()
25641 found = clear_start(found,startdiscard); in prev_dinucleotide_position()
25643 if (found != 0U) { in prev_dinucleotide_position()
25645 foundpos = offset - (relpos = __builtin_clz(found)); in prev_dinucleotide_position()
25647 foundpos = offset - (relpos = (top = found >> 16) ? clz_table[top] : 16 + clz_table[found]); in prev_dinucleotide_position()
25650 found,(unsigned long long) offset,relpos,(unsigned long long) (foundpos-chroffset), in prev_dinucleotide_position()
25673 Genomecomp_T found;
25707 found = block_find_snp(&high_halfsite,&low_halfsite,
25710 found = block_find(&high_halfsite,&low_halfsite,&(ref_blocks[startblocki]),splicesite_bits);
25712 found = clear_start(found,startdiscard);
25713 found = clear_end(found,enddiscard);
25716 while (found != 0U) {
25718 pos = offset + (relpos = __builtin_ctz(found));
25725 clear_lowbit(found,relpos);
25727 debug3(printf("found is %08X, -found & found is %08X\n",found,-found & found));
25728 pos = offset + mod_37_bit_position[(lowbit = -found & found) % 37];
25735 found -= lowbit;
25738 found,(unsigned long long) offset,relpos));
25752 found = block_find_snp(&high_halfsite,&low_halfsite,
25755 found = block_find(&high_halfsite,&low_halfsite,&(ref_blocks[startblocki]),splicesite_bits);
25757 found = clear_start(found,startdiscard);
25760 while (found != 0U) {
25762 pos = offset + (relpos = __builtin_ctz(found));
25769 clear_lowbit(found,relpos);
25771 debug3(printf("found is %08X, -found & found is %08X\n",found,-found & found));
25772 pos = offset + mod_37_bit_position[(lowbit = -found & found) % 37];
25779 found -= lowbit;
25782 found,(unsigned long long) offset,relpos));
25792 found = block_find_snp(&high_halfsite,&low_halfsite,ptr,altptr,splicesite_bits);
25794 found = block_find(&high_halfsite,&low_halfsite,ptr,splicesite_bits);
25807 while (found != 0U) {
25809 pos = offset + (relpos = __builtin_ctz(found));
25816 clear_lowbit(found,relpos);
25818 debug3(printf("found is %08X, -found & found is %08X\n",found,-found & found));
25819 pos = offset + mod_37_bit_position[(lowbit = -found & found) % 37];
25826 found -= lowbit;
25829 found,(unsigned long long) offset,relpos));
25840 found = block_find_snp(&high_halfsite,&low_halfsite,ptr,altptr,splicesite_bits);
25842 found = block_find(&high_halfsite,&low_halfsite,ptr,splicesite_bits);
25844 found = clear_end(found,enddiscard);
25857 while (found != 0U) {
25859 pos = offset + (relpos = __builtin_ctz(found));
25866 clear_lowbit(found,relpos);
25868 debug3(printf("found is %08X, -found & found is %08X\n",found,-found & found));
25869 pos = offset + mod_37_bit_position[(lowbit = -found & found) % 37];
25876 found -= lowbit;
25879 found,(unsigned long long) offset,relpos));
25904 Genomecomp_T found;
25929 found = block_find_snp(&high_halfsite,&low_halfsite,
25932 found = block_find(&high_halfsite,&low_halfsite,&(ref_blocks[startblocki]),splicesite_bits);
25934 found = clear_start(found,startdiscard);
25936 found = clear_end(found,enddiscard);
25938 if (found != 0U) {
25940 foundpos = offset - (relpos = __builtin_ctz(found));
25942 foundpos = offset - (relpos = mod_37_bit_position[(lowbit = -found & found) % 37]);
25945 found,(unsigned long long) offset,relpos,(unsigned long long) (chrhigh - foundpos)));
25953 found = block_find(&high_halfsite,&low_halfsite,&(ref_blocks[startblocki]),splicesite_bits);
25954 found = clear_start(found,startdiscard);
25956 if (found != 0U) {
25958 foundpos = offset - (relpos = __builtin_ctz(found));
25960 foundpos = offset - (relpos = mod_37_bit_position[(lowbit = -found & found) % 37]);
25963 found,(unsigned long long) offset,relpos,(unsigned long long) (chrhigh-foundpos)));
25976 found = block_find_snp(&high_halfsite,&low_halfsite,ptr,altptr,splicesite_bits);
25978 found = block_find(&high_halfsite,&low_halfsite,ptr,splicesite_bits);
25985 } else if (found != 0U) {
25987 foundpos = offset - (relpos = __builtin_ctz(found));
25989 foundpos = offset - (relpos = mod_37_bit_position[(lowbit = -found & found) % 37]);
25992 found,(unsigned long long) offset,relpos,(unsigned long long) (chrhigh-foundpos)));
26004 found = block_find_snp(&high_halfsite,&low_halfsite,ptr,altptr,splicesite_bits);
26006 found = block_find(&high_halfsite,&low_halfsite,ptr,splicesite_bits);
26015 found = clear_end(found,enddiscard);
26017 if (found != 0U) {
26019 foundpos = offset - (relpos = __builtin_ctz(found));
26021 foundpos = offset - (relpos = mod_37_bit_position[(lowbit = -found & found) % 37]);
26024 found,(unsigned long long) offset,relpos,(unsigned long long) (chrhigh-foundpos)));
26044 Genomecomp_T found;
26081 found = block_find_snp(&high_halfsite,&low_halfsite,
26084 found = block_find(&high_halfsite,&low_halfsite,&(ref_blocks[startblocki]),splicesite_bits);
26086 found = clear_start(found,startdiscard);
26087 found = clear_end(found,enddiscard);
26090 while (found != 0U) {
26092 pos = offset - (relpos = __builtin_ctz(found));
26098 clear_lowbit(found,relpos);
26100 debug3(printf("found is %08X, -found & found is %08X\n",found,-found & found));
26101 pos = offset - mod_37_bit_position[(lowbit = -found & found) % 37];
26107 found -= lowbit;
26109 debug3(printf("found is %08X => offset %u - relpos %d\n",found,offset,relpos));
26124 found = block_find_snp(&high_halfsite,&low_halfsite,
26127 found = block_find(&high_halfsite,&low_halfsite,&(ref_blocks[startblocki]),splicesite_bits);
26129 found = clear_start(found,startdiscard);
26132 while (found != 0U) {
26134 pos = offset - (relpos = __builtin_ctz(found));
26140 clear_lowbit(found,relpos);
26142 debug3(printf("found is %08X, -found & found is %08X\n",found,-found & found));
26143 pos = offset - mod_37_bit_position[(lowbit = -found & found) % 37];
26149 found -= lowbit;
26151 debug3(printf("found is %08X => offset %u - relpos %d\n",found,offset,relpos));
26161 found = block_find_snp(&high_halfsite,&low_halfsite,ptr,altptr,splicesite_bits);
26163 found = block_find(&high_halfsite,&low_halfsite,ptr,splicesite_bits);
26175 while (found != 0U) {
26177 pos = offset - (relpos = __builtin_ctz(found));
26183 clear_lowbit(found,relpos);
26185 debug3(printf("found is %08X, -found & found is %08X\n",found,-found & found));
26186 pos = offset - mod_37_bit_position[(lowbit = -found & found) % 37];
26192 found -= lowbit;
26194 debug3(printf("found is %08X => offset %u - relpos %d\n",found,offset,relpos));
26205 found = block_find_snp(&high_halfsite,&low_halfsite,ptr,altptr,splicesite_bits);
26207 found = block_find(&high_halfsite,&low_halfsite,ptr,splicesite_bits);
26209 found = clear_end(found,enddiscard);
26210 debug3(printf("adding end mask %08x => found %08x\n",clear_end_mask(enddiscard),found));
26221 while (found != 0U) {
26223 pos = offset - (relpos = __builtin_ctz(found));
26229 clear_lowbit(found,relpos);
26231 debug3(printf("found is %08X, -found & found is %08X\n",found,-found & found));
26232 pos = offset - mod_37_bit_position[(lowbit = -found & found) % 37];
26238 found -= lowbit;
26240 debug3(printf("found is %08X => offset %u - relpos %d\n",found,offset,relpos));