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Searched refs:max_cov (Results 1 – 6 of 6) sorted by relevance

/dports/biology/py-multiqc/multiqc-1.10/multiqc/modules/picard/
H A DWgsMetrics.py149 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:
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/sra/readers/bam/
H A Dbamgraph.cpp556 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()
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/dports/biology/velvet/velvet_1.2.10/contrib/show_repeats/
H A Dshow_repeats.pl73 my $expcov = max_cov($cov);
171 sub max_cov
/dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/src/tigr/
H A Dshow-tiling.cc1129 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()
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/dports/biology/py-ete3/ete3-3.1.2/ete3/tools/ete_build_lib/task/
H A Dcog_creator.py471 …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
/dports/biology/ncbi-cxx-toolkit/ncbi_cxx--25_2_0/src/algo/gnomon/
H A Dchainer.cpp5682 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()