/dports/devel/plan9port/plan9port-1f098efb7370a0b28306d10681e21883fb1c1507/src/cmd/venti/srv/ |
H A D | arena.c | 371 arena->ncig = -1; in writeaclump() 804 u32int i, j, ncig, nci; in loadcig() local 816 if(ncig == 0){ in loadcig() 818 arena->ncig = 0; in loadcig() 826 for(i=0; i<ncig; i++){ in loadcig() 832 if(i != ncig-1){ in loadcig() 835 arena->ncig = -1; in loadcig() 843 arena->ncig = ncig; in loadcig() 868 r = arena->ncig - 1; in arenatog() 880 if(l+1 < arena->ncig) in arenatog() [all …]
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H A D | dat.h | 387 int ncig; member
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/dports/biology/py-pysam/pysam-0.18.0/samtools/ |
H A D | stats.c | 419 icycle += ncig; in count_indels() 438 icycle += ncig; in count_indels() 468 iread += ncig; in count_mismatches_per_cycle() 469 icycle += ncig; in count_mismatches_per_cycle() 474 iref += ncig; in count_mismatches_per_cycle() 479 icycle += ncig; in count_mismatches_per_cycle() 482 iread += ncig; in count_mismatches_per_cycle() 487 icycle += ncig; in count_mismatches_per_cycle() 1276 else if ( iref+ncig-1 > stats->reg_to ) ncig -= iref+ncig-1 - stats->reg_to; in collect_stats() 1277 if ( ncig<0 ) ncig = 0; in collect_stats() [all …]
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H A D | stats.c.pysam.c | 421 icycle += ncig; in count_indels() 440 icycle += ncig; in count_indels() 470 iread += ncig; in count_mismatches_per_cycle() 471 icycle += ncig; in count_mismatches_per_cycle() 476 iref += ncig; in count_mismatches_per_cycle() 481 icycle += ncig; in count_mismatches_per_cycle() 484 iread += ncig; in count_mismatches_per_cycle() 489 icycle += ncig; in count_mismatches_per_cycle() 1278 else if ( iref+ncig-1 > stats->reg_to ) ncig -= iref+ncig-1 - stats->reg_to; in collect_stats() 1279 if ( ncig<0 ) ncig = 0; in collect_stats() [all …]
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H A D | bam2bcf.c | 88 int ncig = bam_get_cigar(p->b)[icig] >> BAM_CIGAR_SHIFT; in get_position() local 91 n_tot_bases += ncig; in get_position() 92 iread += ncig; in get_position() 97 n_tot_bases += ncig; in get_position() 98 iread += ncig; in get_position() 103 iread += ncig; in get_position() 104 if ( iread<=p->qpos ) edist -= ncig; in get_position()
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H A D | bam2bcf.c.pysam.c | 90 int ncig = bam_get_cigar(p->b)[icig] >> BAM_CIGAR_SHIFT; in get_position() local 93 n_tot_bases += ncig; in get_position() 94 iread += ncig; in get_position() 99 n_tot_bases += ncig; in get_position() 100 iread += ncig; in get_position() 105 iread += ncig; in get_position() 106 if ( iread<=p->qpos ) edist -= ncig; in get_position()
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H A D | bam2depth.c | 325 int ncig = b->core.n_cigar, j, k, spos = 0; in add_depth() local 340 for (j = 0; j < ncig; j++) { in add_depth()
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H A D | bam2depth.c.pysam.c | 327 int ncig = b->core.n_cigar, j, k, spos = 0; in add_depth() local 342 for (j = 0; j < ncig; j++) { in add_depth()
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/dports/biology/samtools/samtools-1.14/ |
H A D | stats.c | 419 icycle += ncig; in count_indels() 438 icycle += ncig; in count_indels() 468 iread += ncig; in count_mismatches_per_cycle() 469 icycle += ncig; in count_mismatches_per_cycle() 474 iref += ncig; in count_mismatches_per_cycle() 479 icycle += ncig; in count_mismatches_per_cycle() 482 iread += ncig; in count_mismatches_per_cycle() 487 icycle += ncig; in count_mismatches_per_cycle() 1276 else if ( iref+ncig-1 > stats->reg_to ) ncig -= iref+ncig-1 - stats->reg_to; in collect_stats() 1277 if ( ncig<0 ) ncig = 0; in collect_stats() [all …]
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H A D | bam2bcf.c | 88 int ncig = bam_get_cigar(p->b)[icig] >> BAM_CIGAR_SHIFT; in get_position() local 91 n_tot_bases += ncig; in get_position() 92 iread += ncig; in get_position() 97 n_tot_bases += ncig; in get_position() 98 iread += ncig; in get_position() 103 iread += ncig; in get_position() 104 if ( iread<=p->qpos ) edist -= ncig; in get_position()
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H A D | bam2depth.c | 325 int ncig = b->core.n_cigar, j, k, spos = 0; in add_depth() local 340 for (j = 0; j < ncig; j++) { in add_depth()
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/dports/biology/kallisto/kallisto-0.46.1/src/ |
H A D | ProcessReads.cpp | 2411 int ncig = tra.cigar.size(); in fixCigarStringGenome() local 2412 if (ncig == 1) { in fixCigarStringGenome() 2436 b.l_data += ((int)(ncig - b.core.n_cigar))*sizeof(uint32_t); in fixCigarStringGenome() 2437 b.core.n_cigar = ncig; in fixCigarStringGenome() 2439 for (int i = 0; i < ncig; i++) { in fixCigarStringGenome() 2446 int ncig = 1; in fixCigarStringTrans() local 2450 ncig = 3; in fixCigarStringTrans() 2452 ncig = 2; in fixCigarStringTrans() 2455 ncig = 2; in fixCigarStringTrans() 2457 if (ncig == 1) { in fixCigarStringTrans() [all …]
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/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/ |
H A D | sam.c | 2035 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_set() local 2037 if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 2041 pos -= ncig; in cigar_iref2iseq_set() 2043 (*cigar)++; *iseq += ncig; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 2046 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 2049 pos -= ncig; in cigar_iref2iseq_set() 2051 (*cigar)++; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 2065 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_next() local 2069 if ( *icig >= ncig - 1 ) { *icig = 0; (*cigar)++; continue; } in cigar_iref2iseq_next() 2074 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_next() [all …]
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/dports/biology/vt/vt-0.57721/lib/htslib/ |
H A D | sam.c | 2276 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_set() local 2278 if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 2282 pos -= ncig; in cigar_iref2iseq_set() 2284 (*cigar)++; *iseq += ncig; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 2287 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 2290 pos -= ncig; in cigar_iref2iseq_set() 2292 (*cigar)++; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 2306 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_next() local 2310 if ( *icig >= ncig - 1 ) { *icig = 0; (*cigar)++; continue; } in cigar_iref2iseq_next() 2315 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_next() [all …]
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/dports/biology/stacks/stacks-2.4/htslib/ |
H A D | sam.c | 2269 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_set() local 2271 if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 2275 pos -= ncig; in cigar_iref2iseq_set() 2277 (*cigar)++; *iseq += ncig; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 2280 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 2283 pos -= ncig; in cigar_iref2iseq_set() 2285 (*cigar)++; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 2299 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_next() local 2303 if ( *icig >= ncig - 1 ) { *icig = 0; (*cigar)++; continue; } in cigar_iref2iseq_next() 2308 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_next() [all …]
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/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/ |
H A D | sam.c | 2446 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_set() local 2448 if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 2452 pos -= ncig; in cigar_iref2iseq_set() 2454 (*cigar)++; *iseq += ncig; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 2457 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 2460 pos -= ncig; in cigar_iref2iseq_set() 2462 (*cigar)++; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 2476 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_next() local 2480 if ( *icig >= ncig - 1 ) { *icig = 0; (*cigar)++; continue; } in cigar_iref2iseq_next() 2485 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_next() [all …]
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/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/ |
H A D | sam.c | 4424 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_set() local 4426 if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 4430 pos -= ncig; in cigar_iref2iseq_set() 4432 (*cigar)++; *iseq += ncig; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 4435 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 4438 pos -= ncig; in cigar_iref2iseq_set() 4440 (*cigar)++; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 4454 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_next() local 4458 if ( *icig >= ncig - 1 ) { *icig = 0; (*cigar)++; continue; } in cigar_iref2iseq_next() 4463 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_next() [all …]
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/dports/biology/py-pysam/pysam-0.18.0/htslib/ |
H A D | sam.c | 5391 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_set() local 5393 if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 5397 pos -= ncig; in cigar_iref2iseq_set() 5399 (*cigar)++; *iseq += ncig; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 5402 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 5405 pos -= ncig; in cigar_iref2iseq_set() 5407 (*cigar)++; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 5425 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_next() local 5429 if ( *icig >= ncig - 1 ) { *icig = -1; (*cigar)++; continue; } in cigar_iref2iseq_next() 5434 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = -1; continue; } in cigar_iref2iseq_next() [all …]
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/dports/biology/htslib/htslib-1.14/ |
H A D | sam.c | 5391 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_set() local 5393 if ( cig==BAM_CSOFT_CLIP ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 5397 pos -= ncig; in cigar_iref2iseq_set() 5399 (*cigar)++; *iseq += ncig; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 5402 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = 0; continue; } in cigar_iref2iseq_set() 5405 pos -= ncig; in cigar_iref2iseq_set() 5407 (*cigar)++; *icig = 0; *iref += ncig; in cigar_iref2iseq_set() 5425 int ncig = (**cigar) >> BAM_CIGAR_SHIFT; in cigar_iref2iseq_next() local 5429 if ( *icig >= ncig - 1 ) { *icig = -1; (*cigar)++; continue; } in cigar_iref2iseq_next() 5434 if ( cig==BAM_CINS ) { (*cigar)++; *iseq += ncig; *icig = -1; continue; } in cigar_iref2iseq_next() [all …]
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/dports/biology/bcftools/bcftools-1.14/ |
H A D | mpileup.c | 476 int ncig = b->core.n_cigar; in mplp_realn() local 482 if ((flag & MPLP_REALN_PARTIAL) && nt > 15 && ncig > 1) { in mplp_realn() 486 for (k = 0; k < ncig; k++) { in mplp_realn() 498 for (k = ncig-1; k >= 0; k--) { in mplp_realn()
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/dports/biology/bio-mocha/bcftools-1.14/ |
H A D | mpileup.c | 476 int ncig = b->core.n_cigar; in mplp_realn() local 482 if ((flag & MPLP_REALN_PARTIAL) && nt > 15 && ncig > 1) { in mplp_realn() 486 for (k = 0; k < ncig; k++) { in mplp_realn() 498 for (k = ncig-1; k >= 0; k--) { in mplp_realn()
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/dports/biology/py-pysam/pysam-0.18.0/bcftools/ |
H A D | mpileup.c | 476 int ncig = b->core.n_cigar; in mplp_realn() local 482 if ((flag & MPLP_REALN_PARTIAL) && nt > 15 && ncig > 1) { in mplp_realn() 486 for (k = 0; k < ncig; k++) { in mplp_realn() 498 for (k = ncig-1; k >= 0; k--) { in mplp_realn()
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H A D | mpileup.c.pysam.c | 478 int ncig = b->core.n_cigar; in mplp_realn() local 484 if ((flag & MPLP_REALN_PARTIAL) && nt > 15 && ncig > 1) { in mplp_realn() 488 for (k = 0; k < ncig; k++) { in mplp_realn() 500 for (k = ncig-1; k >= 0; k--) { in mplp_realn()
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/dports/graphics/grads/grads-1.9b4/src/ |
H A D | gaio.c | 1727 int rc,i,j,ig,ioff,ix,iy,ncig,ncjg; in gaprow() local 1794 ncig = (int)(1 + ioff%pfi->ppisiz); in gaprow() 1796 rc = ganrow(ncig,ncjg,z,tt,2,p); /* PDEF BILIN for netcdf */ in gaprow() 1813 rc = ganrow(ncig,ncjg,z,tt,2,p+2); /* PDEF BILIN for netcdf */ in gaprow()
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/dports/biology/subread/subread-2.0.2-source/src/ |
H A D | input-files.c | 1372 char ncig[EXON_MAX_CIGAR_LEN]; in fix_cigar_SAM14() local 1385 wi += sprintf(ncig + wi, "%dM", tmpM); in fix_cigar_SAM14() 1389 else wi += sprintf(ncig + wi, "%d%c", tmpi, nch); in fix_cigar_SAM14() 1395 memcpy(cig, ncig, wi+1); in fix_cigar_SAM14()
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