/dports/biology/gatk/gatk-4.2.0.0/src/main/python/org/broadinstitute/hellbender/gcnvkernel/structs/ |
H A D | interval.py | 96 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
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/dports/biology/py-cutadapt/cutadapt-3.3/src/cutadapt/ |
H A D | report.py | 230 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 …]
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/ |
H A D | SelectionViewer.java | 180 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()
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/dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/sraxf/ |
H A D | stat_mod.c | 144 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()
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H A D | stat_mod.h | 56 uint8_t gc_content; member
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/dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/sraxf/ |
H A D | stat_mod.c | 144 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()
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H A D | stat_mod.h | 56 uint8_t gc_content; member
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/dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/plot/ |
H A D | GCSDWindowAlgorithm.java | 104 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()
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/dports/biology/sra-tools/sra-tools-2.11.0/tools/qual-recalib-stat/ |
H A D | stat_mod_1.c | 193 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()
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H A D | stat_mod_2.c | 342 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()
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H A D | stat_mod.c | 260 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()
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H A D | stat_mod_2.h | 99 uint8_t gc_content; member
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H A D | stat_mod.h | 89 uint32_t gc_content; member
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H A D | stat_mod_1.h | 90 uint8_t gc_content; member
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/dports/biology/primer3/primer3-2.3.6/test/primer_global_err/ |
H A D | pr_gc_content_obj_fn.out2 | 1 ../src/primer3_core: Primer GC content is part of objective function while optimum gc_content is no…
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H A D | io_gc_content_obj_fn.out2 | 1 ../src/primer3_core: Hyb probe GC content is part of objective function while optimum gc_content is…
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H A D | pr_gc_content_obj_fn.out | 25 PRIMER_ERROR=Primer GC content is part of objective function while optimum gc_content is not defined
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H A D | io_gc_content_obj_fn.out | 27 PRIMER_ERROR=Hyb probe GC content is part of objective function while optimum gc_content is not def…
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/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/ngs_roi/tests/ |
H A D | out_mrna_2l.roi | 2 ##ref begin_pos end_pos region_name length strand max_count num_reads gc_content counts
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H A D | out_mrna_2l_ss.roi | 2 ##ref begin_pos end_pos region_name length strand max_count num_reads gc_content counts
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/dports/biology/ugene/ugene-40.1/src/corelibs/U2Core/src/datatype/ |
H A D | U2CoreAttributes.h | 53 static const QString gc_content; // = "GC-content"; variable
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/dports/biology/prodigal/Prodigal-2.6.3-7-ga78ed3f/ |
H A D | sequence.h | 69 double gc_content(unsigned char *, int, int);
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/dports/biology/ugene/ugene-40.1/src/plugins_3rdparty/primer3/src/primer3_core/ |
H A D | primer3_main.c | 849 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 …]
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/dports/biology/primer3/primer3-2.3.6/src/ |
H A D | print_boulder.c | 295 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()
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/dports/biology/py-scikit-bio/scikit-bio-0.5.6/benchmarks/ |
H A D | benchmarks.py | 61 dna_seq.gc_content()
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