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Searched refs:ncig (Results 1 – 25 of 33) sorted by relevance

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/dports/devel/plan9port/plan9port-1f098efb7370a0b28306d10681e21883fb1c1507/src/cmd/venti/srv/
H A Darena.c371 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 …]
H A Ddat.h387 int ncig; member
/dports/biology/py-pysam/pysam-0.18.0/samtools/
H A Dstats.c419 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 …]
H A Dstats.c.pysam.c421 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 …]
H A Dbam2bcf.c88 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()
H A Dbam2bcf.c.pysam.c90 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()
H A Dbam2depth.c325 int ncig = b->core.n_cigar, j, k, spos = 0; in add_depth() local
340 for (j = 0; j < ncig; j++) { in add_depth()
H A Dbam2depth.c.pysam.c327 int ncig = b->core.n_cigar, j, k, spos = 0; in add_depth() local
342 for (j = 0; j < ncig; j++) { in add_depth()
/dports/biology/samtools/samtools-1.14/
H A Dstats.c419 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 …]
H A Dbam2bcf.c88 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()
H A Dbam2depth.c325 int ncig = b->core.n_cigar, j, k, spos = 0; in add_depth() local
340 for (j = 0; j < ncig; j++) { in add_depth()
/dports/biology/kallisto/kallisto-0.46.1/src/
H A DProcessReads.cpp2411 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 …]
/dports/biology/kallisto/kallisto-0.46.1/ext/htslib/
H A Dsam.c2035 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 …]
/dports/biology/vt/vt-0.57721/lib/htslib/
H A Dsam.c2276 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 …]
/dports/biology/stacks/stacks-2.4/htslib/
H A Dsam.c2269 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 …]
/dports/biology/bedtools/bedtools2-2.30.0/src/utils/htslib/
H A Dsam.c2446 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 …]
/dports/biology/freebayes/freebayes-1.3.5/contrib/htslib/
H A Dsam.c4424 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 …]
/dports/biology/py-pysam/pysam-0.18.0/htslib/
H A Dsam.c5391 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 …]
/dports/biology/htslib/htslib-1.14/
H A Dsam.c5391 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 …]
/dports/biology/bcftools/bcftools-1.14/
H A Dmpileup.c476 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()
/dports/biology/bio-mocha/bcftools-1.14/
H A Dmpileup.c476 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()
/dports/biology/py-pysam/pysam-0.18.0/bcftools/
H A Dmpileup.c476 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()
H A Dmpileup.c.pysam.c478 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()
/dports/graphics/grads/grads-1.9b4/src/
H A Dgaio.c1727 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()
/dports/biology/subread/subread-2.0.2-source/src/
H A Dinput-files.c1372 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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