Searched refs:max_cov (Results 1 – 6 of 6) sorted by relevance
/dports/biology/py-multiqc/multiqc-1.10/multiqc/modules/picard/ |
H A D | WgsMetrics.py | 149 max_cov = picard_config.get("wgsmetrics_histogram_max_cov") 150 if max_cov is None: 151 max_cov = 10 158 max_cov = max(k, max_cov) 171 if k <= max_cov:
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/bam/ |
H A D | bamgraph.cpp | 556 Uint8 min_cov = kMax_UI8, max_cov = 0, sum_cov = 0; in MakeSeq_annot() local 566 if ( c > max_cov ) { in MakeSeq_annot() 567 max_cov = c; in MakeSeq_annot() 575 max_cov = 2; in MakeSeq_annot() 595 user_desc.AddField("MaxCoverage", max_cov*cov_mul); in MakeSeq_annot() 599 if ( max_cov > avg_cov*GetOutlierMax() ) { in MakeSeq_annot() 600 max_cov = Uint8(avg_cov*GetOutlierMax()); in MakeSeq_annot() 601 user_desc.AddField("LimitCoverage", max_cov*cov_mul); in MakeSeq_annot() 654 else if ( c > max_cov ) { in MakeSeq_annot() 676 double byte_mul = double(MAX-1)/(max_cov-min_cov); in MakeSeq_annot() [all …]
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/dports/biology/velvet/velvet_1.2.10/contrib/show_repeats/ |
H A D | show_repeats.pl | 73 my $expcov = max_cov($cov); 171 sub max_cov
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/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/src/tigr/ |
H A D | show-tiling.cc | 1129 float max_cov, cov; in placeContig() local 1136 max_cov = -(FLT_MAX); in placeContig() 1146 if ( cov > max_cov ) in placeContig() 1148 max_cov = cov; in placeContig() 1532 float max_cov, maxx_cov; in tileContigs() local 1542 max_cov = maxx_cov = idy = -(FLT_MAX); in tileContigs() 1582 if ( cov >= max_cov ) in tileContigs() 1585 if ( cov > max_cov || (cov == max_cov && tmpidy > idy) ) in tileContigs() 1588 maxx_cov = max_cov; in tileContigs() 1589 max_cov = cov; in tileContigs() [all …]
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/dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ete_build_lib/task/ |
H A D | cog_creator.py | 471 …score, min_cov, max_cov, median_cov, cov_std, cog_cov = get_cog_score(candidates, sp2hits, median_… 530 max_cov = _min(sp_coverages) 532 return min_cov, max_cov, median_cov 546 max_cov = _min(sp_coverages) 551 return score, min_cov, max_cov, median_cov, cov_std, cog_cov
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/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/ |
H A D | chainer.cpp | 5682 double max_cov = 0; in CalculateDropLimits() local 5684 max_cov = max(max_cov,m_coverage[left_limit]); in CalculateDropLimits() 5685 if(max_cov > m_core_coverage*COVERAGE_BUMP) in CalculateDropLimits() 5718 double max_cov = 0; in CalculateDropLimits() local 5720 max_cov = max(max_cov,m_coverage[right_limit]); in CalculateDropLimits() 5721 if(first_bump < 0 && max_cov > m_core_coverage*COVERAGE_BUMP) in CalculateDropLimits()
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