| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/mason2/ |
| H A D | individual_genome.h | 138 GenomeVariantManager(unsigned numContigs) : _numContigs(numContigs) in GenomeVariantManager() argument
151 unsigned numContigs() const;
|
| H A D | external_split_merge.h | 122 unsigned numContigs;
129 IdSplitter() : numContigs(0) in IdSplitter()
132 IdSplitter(unsigned numContigs) : numContigs(numContigs) in IdSplitter() argument
|
| H A D | external_split_merge.cpp | 44 for (unsigned i = 0; i < numContigs; ++i) in open()
|
| H A D | mason_simulator.cpp | 1085 alignmentSplitter.numContigs = fragmentIdSplitter.numContigs; in _initAlignmentSplitter()
1138 fragmentIdSplitter.numContigs = numSeqs(vcfMat.faiIndex) * vcfMat.numHaplotypes; in _initContigPicker()
1141 fragmentSplitter.numContigs = fragmentIdSplitter.numContigs; in _initContigPicker()
|
| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/demos/tutorial/simple_rna_seq/ |
| H A D | genequant_solution3.cpp | 82 int numContigs = length(intervals); in constructIntervalTrees() local
83 resize(intervalTrees, numContigs); in constructIntervalTrees()
86 for (int i = 0; i < numContigs; ++i) in constructIntervalTrees()
|
| H A D | genequant_assignment4.cpp | 86 int numContigs = length(intervals); in constructIntervalTrees() local
87 resize(intervalTrees, numContigs); in constructIntervalTrees()
90 for (int i = 0; i < numContigs; ++i) in constructIntervalTrees()
|
| H A D | genequant_assignment5.cpp | 87 int numContigs = length(intervals); in constructIntervalTrees() local
88 resize(intervalTrees, numContigs); in constructIntervalTrees()
91 for (int i = 0; i < numContigs; ++i) in constructIntervalTrees()
|
| H A D | genequant_solution4.cpp | 83 int numContigs = length(intervals); in constructIntervalTrees() local
84 resize(intervalTrees, numContigs); in constructIntervalTrees()
87 for (int i = 0; i < numContigs; ++i) in constructIntervalTrees()
|
| H A D | genequant_solution5.cpp | 83 int numContigs = length(intervals); in constructIntervalTrees() local
84 resize(intervalTrees, numContigs); in constructIntervalTrees()
87 for (int i = 0; i < numContigs; ++i) in constructIntervalTrees()
|
| /dports/biology/checkm/CheckM-1.0.18/checkm/test/ |
| H A D | test_genomicSignatures.py | 51 …maxScaffoldLen, maxContigLen, totalScaffoldBps, _, _, numContigs = binStats.calculateScaffoldLengt…
60 self.assertAlmostEqual(numContigs, 4)
|
| /dports/biology/py-biopython/biopython-1.79/Tests/codonalign/ |
| H A D | nucl2.fa | 1 >isotig35100 gene=isogroup05278 length=3411 numContigs=3
57 >isotig35101 gene=isogroup05278 length=3391 numContigs=3
|
| H A D | nucl3.fa | 291 >isotig12565 gene=isogroup02894 length=2436 numContigs=2
333 >isotig12566 gene=isogroup02894 length=2402 numContigs=2
374 >isotig46679 gene=isogroup11619 length=3088 numContigs=1
|
| H A D | nucl4.fa | 291 >isotig12565 gene=isogroup02894 length=2436 numContigs=2
333 >isotig12566 gene=isogroup02894 length=2402 numContigs=2
374 >isotig46679 gene=isogroup11619 length=3088 numContigs=1
|
| H A D | nucl1.fa | 1 >isotig69710 gene=isogroup34650 length=560 numContigs=1
|
| H A D | nucl5.fa | 1 >isotig69710 gene=isogroup34650 length=560 numContigs=1
|
| /dports/biology/groopm/GroopM-0.3.4/groopm/ |
| H A D | mstore.py | 850 expectedrows=CT.numContigs)
866 expectedrows=CT.numContigs)
893 expectedrows=CT.numContigs)
1789 numContigs, argument
1796 self.numContigs = numContigs
1802 self.indices = range(self.numContigs)
1807 self.transformedCP = np.zeros((self.numContigs,3))
1899 sub_cons = np.arange(self.numContigs)
|
| H A D | profileManager.py | 150 self.numContigs = 0 # this depends on the condition given
192 self.numContigs = len(self.indices)
194 if self.numContigs == 0:
199 print " Working with: %d contigs" % self.numContigs
|
| H A D | refine.py | 155 perc = "%.2f" % round((float(num_binned)/float(self.PM.numContigs))*100,2)
168 perc = "%.2f" % round((float(num_binned)/float(self.PM.numContigs))*100,2)
|
| H A D | binManager.py | 175 if self.PM.numContigs == 0:
|
| /dports/biology/checkm/CheckM-1.0.18/checkm/ |
| H A D | binStatistics.py | 121 …n, genomeSize, scaffold_N50, contig_N50, scaffoldAvgLen, contigAvgLen, numContigs, numAmbiguousBas…
125 binStats['# contigs'] = numContigs
|
| /dports/biology/abyss/abyss-2.3.1/PopBubbles/ |
| H A D | PopBubbles.cpp | 692 size_t numContigs = num_vertices(g) / 2; in main() local
700 ContigNode u(numContigs + it - paths.begin(), false); in main()
711 ContigNode u(numContigs + it - paths.begin(), false); in main()
|
| /dports/biology/gatk/gatk-4.2.0.0/src/testUtils/java/org/broadinstitute/hellbender/testutils/ |
| H A D | ReadsPreprocessingPipelineTestData.java | 211 …public static List<GATKRead> makeReferenceShardBoundaryReads( final int numContigs, final int numS… in makeReferenceShardBoundaryReads() argument
215 for ( int contig = 1; contig <= numContigs; ++contig ) { in makeReferenceShardBoundaryReads()
|
| /dports/biology/bbmap/bbmap/current/dna/ |
| H A D | Data.java | 50 numContigs=0; in unloadAll()
782 numContigs=-1; in setGenome2()
808 else if(a.equalsIgnoreCase("contigs")){numContigs=Integer.parseInt(b);} in setGenome2()
837 else if(a.equalsIgnoreCase("contigs")){numContigs=Integer.parseInt(b);} in setGenome2()
1274 public static int numContigs; local
|
| /dports/biology/abyss/abyss-2.3.1/FilterGraph/ |
| H A D | FilterGraph.cc | 817 size_t numContigs = num_vertices(g) / 2; in main() local
826 ContigNode u(numContigs + it - paths.begin(), false); in main()
|
| /dports/biology/abyss/abyss-2.3.1/MergePaths/ |
| H A D | PathConsensus.cpp | 308 size_t numContigs = num_vertices(g) / 2; in outputNewContig() local
309 ContigNode u(numContigs + g_newVertices.size(), false); in outputNewContig()
|