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Searched refs:gc_content (Results 1 – 25 of 56) sorted by relevance

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/dports/biology/gatk/gatk-4.2.0.0/src/main/python/org/broadinstitute/hellbender/gcnvkernel/structs/
H A Dinterval.py96 def __init__(self, gc_content): argument
97 super().__init__(gc_content)
101 gc_content = float(raw_value)
102 if not 0.0 <= gc_content <= 1.0:
103 raise ValueError("GC content ({0}) must be a float in range [0, 1]".format(gc_content))
104 return gc_content
/dports/biology/py-cutadapt/cutadapt-3.3/src/cutadapt/
H A Dreport.py230 def histogram(end_statistics: EndStatistics, n: int, gc_content: float) -> str:
243 match_probabilities = end_statistics.random_match_probabilities(gc_content=gc_content)
305 def full_report(stats: Statistics, time: float, gc_content: float) -> str: # noqa: C901
422 print_s(histogram(adapter_statistics.front, stats.n, gc_content))
425 print_s(histogram(adapter_statistics.back, stats.n, gc_content))
431 print_s(histogram(adapter_statistics.front, stats.n, gc_content))
434 print_s(histogram(adapter_statistics.back, stats.n, gc_content))
439 print_s(histogram(adapter_statistics.front, stats.n, gc_content))
448 print_s(histogram(adapter_statistics.back, stats.n, gc_content))
458 def minimal_report(stats: Statistics, time: float, gc_content: float) -> str:
[all …]
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/
H A DSelectionViewer.java180 final double gc_content = this_feature.getPercentGC (); in readSelection() local
192 if (min_gc_content > gc_content) { in readSelection()
193 min_gc_content = gc_content; in readSelection()
196 if (max_gc_content < gc_content) { in readSelection()
197 max_gc_content = gc_content; in readSelection()
/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/sraxf/
H A Dstat_mod.c144 uint8_t const gc_content, in spotgroup_enter_values() argument
151 uint8_t g = gc_content; in spotgroup_enter_values()
356 for( ctx->row.gc_content = 0; ctx->row.gc_content < N_GC_VALUES; ++ctx->row.gc_content ) in spotgroup_iter()
361 …counter_vector * cv = &sg->cnv[ dimer_nr ][ ctx->row.gc_content ][ ctx->row.hp_run ][ ctx->row.qua… in spotgroup_iter()
H A Dstat_mod.h56 uint8_t gc_content; member
/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/sraxf/
H A Dstat_mod.c144 uint8_t const gc_content, in spotgroup_enter_values() argument
151 uint8_t g = gc_content; in spotgroup_enter_values()
356 for( ctx->row.gc_content = 0; ctx->row.gc_content < N_GC_VALUES; ++ctx->row.gc_content ) in spotgroup_iter()
361 …counter_vector * cv = &sg->cnv[ dimer_nr ][ ctx->row.gc_content ][ ctx->row.hp_run ][ ctx->row.qua… in spotgroup_iter()
H A Dstat_mod.h56 uint8_t gc_content; member
/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/plot/
H A DGCSDWindowAlgorithm.java104 final float gc_content = gc_count/sequence.length () * 100; in getValues() local
109 if (Math.abs (gc_content - gc_average) < standard_deviation * 2.5) { in getValues()
112 values[0] = gc_content; in getValues()
/dports/biology/sra-tools/sra-tools-2.11.0/tools/qual-recalib-stat/
H A Dstat_mod_1.c193 const uint8_t gc_content, in spotgroup_enter_values() argument
202 uint8_t g = gc_content; in spotgroup_enter_values()
528 uint8_t gc_content = 0; in loop_through_base_calls() local
551 assert( gc_content > 0 ); in loop_through_base_calls()
552 gc_content--; in loop_through_base_calls()
576 gc_content, in loop_through_base_calls()
586 gc_content++; in loop_through_base_calls()
812 for( ctx->row.gc_content = 0; ctx->row.gc_content < N_GC_VALUES; ++ctx->row.gc_content ) in spotgroup_iter()
817 …counter_vector * cv = &sg->cnv[ dimer_nr ][ ctx->row.gc_content ][ ctx->row.hp_run ][ ctx->row.qua… in spotgroup_iter()
922 &row->gc_content, 1, widx_names[ WIDX_GC_CONTENT ] ); in write_cb()
H A Dstat_mod_2.c342 const uint8_t gc_content, in spotgroup_enter_values() argument
353 uint8_t g = gc_content; in spotgroup_enter_values()
634 uint8_t gc_content = 0; in loop_through_base_calls() local
671 assert( gc_content > 0 ); in loop_through_base_calls()
672 gc_content--; in loop_through_base_calls()
696 gc_content, in loop_through_base_calls()
708 gc_content++; in loop_through_base_calls()
947 ctx->row.gc_content = gc; in counter_visit()
1001 ctx->row.gc_content = gc; in spotgroup_iter()
H A Dstat_mod.c260 if ( row->gc_content >= N_GC_VALUES ) in spotgroup_enter_values()
261 row->gc_content = N_GC_VALUES - 1; in spotgroup_enter_values()
265 pv = &sg->dimers[ dimer_idx ][ row->quality ][ row->gc_content ][ row->hp_run ]; in spotgroup_enter_values()
541 assert( row.gc_content > 0 ); in loop_through_base_calls()
542 row.gc_content--; in loop_through_base_calls()
560 row.gc_content++; in loop_through_base_calls()
742 row.gc_content = gc_idx; in spotgroup_iter()
843 &row->gc_content, 1, widx_names[ WIDX_GC_CONTENT ] ); in write_cb()
H A Dstat_mod_2.h99 uint8_t gc_content; member
H A Dstat_mod.h89 uint32_t gc_content; member
H A Dstat_mod_1.h90 uint8_t gc_content; member
/dports/biology/primer3/primer3-2.3.6/test/primer_global_err/
H A Dpr_gc_content_obj_fn.out21 ../src/primer3_core: Primer GC content is part of objective function while optimum gc_content is no…
H A Dio_gc_content_obj_fn.out21 ../src/primer3_core: Hyb probe GC content is part of objective function while optimum gc_content is…
H A Dpr_gc_content_obj_fn.out25 PRIMER_ERROR=Primer GC content is part of objective function while optimum gc_content is not defined
H A Dio_gc_content_obj_fn.out27 PRIMER_ERROR=Hyb probe GC content is part of objective function while optimum gc_content is not def…
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/ngs_roi/tests/
H A Dout_mrna_2l.roi2 ##ref begin_pos end_pos region_name length strand max_count num_reads gc_content counts
H A Dout_mrna_2l_ss.roi2 ##ref begin_pos end_pos region_name length strand max_count num_reads gc_content counts
/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/datatype/
H A DU2CoreAttributes.h53 static const QString gc_content; // = "GC-content"; variable
/dports/biology/prodigal/Prodigal-2.6.3-7-ga78ed3f/
H A Dsequence.h69 double gc_content(unsigned char *, int, int);
/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/primer3/src/primer3_core/
H A Dprimer3_main.c849 h->target = h->gc_content = h->num_ns=h->excl=0;
944 if((l<2 && (h->gc_content< pa->min_gc || h->gc_content > pa->max_gc)) ||
945 (l==2 && (h->gc_content< pa->io_min_gc || h->gc_content > pa->io_max_gc))){
1171 if (0 == num_gcat) h->gc_content= 0.0;
1172 else h->gc_content = 100.0 * ((double)num_gc)/num_gcat;
1208 * (h->gc_content - pa->opt_gc_content);
1211 * (pa->opt_gc_content - h->gc_content);
1256 if(pa->io_weights.gc_content_gt && h->gc_content > pa->io_opt_gc_content)
1258 * (h->gc_content - pa->io_opt_gc_content);
1259 if(pa->io_weights.gc_content_lt && h->gc_content < pa->io_opt_gc_content)
[all …]
/dports/biology/primer3/primer3-2.3.6/src/
H A Dprint_boulder.c295 printf("PRIMER_LEFT%s_GC_PERCENT=%.3f\n", suffix, fwd->gc_content); in print_boulder()
297 printf("PRIMER_RIGHT%s_GC_PERCENT=%.3f\n", suffix, rev->gc_content); in print_boulder()
300 intl->gc_content); in print_boulder()
/dports/biology/py-scikit-bio/scikit-bio-0.5.6/benchmarks/
H A Dbenchmarks.py61 dna_seq.gc_content()

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