| /dports/biology/fastp/fastp-0.23.2/src/ |
| H A D | filterresult.cpp | 316 void FilterResult::reportHtml(ofstream& ofs, long totalReads, long totalBases) { in reportHtml()
336 void FilterResult::reportAdapterHtml(ofstream& ofs, long totalBases) { in reportAdapterHtml()
349 …::outputAdaptersHtml(ofstream& ofs, map<string, long, classcomp>& adapterCounts, long totalBases) { in outputAdaptersHtml() argument
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| /dports/biology/canu/canu-2.2/src/overlapErrorAdjustment/ |
| H A D | fixErrors.C | 132 uint64 totalBases = 0; in main() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/graphs/ |
| H A D | AdaptiveChainPruner.java | 42 …final int totalBases = chains.stream().mapToInt(c -> c.getEdges().stream().mapToInt(E::getMultipli… in chainsToRemove() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/ |
| H A D | PSKmerUtils.java | 49 …final long totalBases = records.values().stream().mapToLong(refBases -> refBases.getBases().length… in getMaskedKmersFromLocalReference() local
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| /dports/biology/sra-tools/sra-tools-2.11.0/ncbi-vdb/libs/ngs/ |
| H A D | SRA_ReferenceSequence.c | 311 uint64_t totalBases = SRA_ReferenceSequenceGetLength ( self, ctx ); in SRA_ReferenceSequenceGetBases() local
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| H A D | EBI_ReferenceSequence.c | 378 uint64_t totalBases = EBI_ReferenceSequenceGetLength ( self, ctx ); in EBI_ReferenceSequenceGetBases() local
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| H A D | CSRA1_Reference.c | 313 uint64_t totalBases = CSRA1_ReferenceGetLength ( self, ctx ); in CSRA1_ReferenceGetBases() local
375 uint64_t totalBases = CSRA1_ReferenceGetLength ( self, ctx ); in CSRA1_ReferenceGetChunk() local
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| /dports/biology/ncbi-vdb/ncbi-vdb-2.11.0/libs/ngs/ |
| H A D | SRA_ReferenceSequence.c | 311 uint64_t totalBases = SRA_ReferenceSequenceGetLength ( self, ctx ); in SRA_ReferenceSequenceGetBases() local
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| H A D | EBI_ReferenceSequence.c | 378 uint64_t totalBases = EBI_ReferenceSequenceGetLength ( self, ctx ); in EBI_ReferenceSequenceGetBases() local
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| H A D | CSRA1_Reference.c | 313 uint64_t totalBases = CSRA1_ReferenceGetLength ( self, ctx ); in CSRA1_ReferenceGetBases() local
375 uint64_t totalBases = CSRA1_ReferenceGetLength ( self, ctx ); in CSRA1_ReferenceGetChunk() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/realignmentfilter/ |
| H A D | FilterAlignmentArtifacts.java | 243 final int totalBases = unitigs.stream().mapToInt(unitig -> unitig.length).sum(); in apply() local
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| /dports/biology/mothur/mothur-1.46.1/source/commands/ |
| H A D | seqerrorcommand.h | 75 int maxLength, totalBases, totalMatches, numRefs; variable
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| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | ReadKmerDepthDistribution.java | 512 long totalBases=0; in downsample() local
1018 private long totalBases=0; field in ReadKmerDepthDistribution.ProcessThread
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| H A D | KmerCoverage.java | 1162 private long totalBases=0; field in KmerCoverage.ProcessThread
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| H A D | KmerNormalize.java | 1617 long totalBases=0; in downsample() local
3435 private long totalBases=0; field in KmerNormalize.ProcessThread
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/contamination/ |
| H A D | ContaminationModel.java | 200 final long totalBases = sites.stream().mapToInt(PileupSummary::getTotalCount).sum(); in calculateErrorRate() local
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| /dports/biology/bbmap/bbmap/current/bloom/ |
| H A D | ErrorCorrect.java | 238 long totalBases=0; in detect() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/ |
| H A D | IntervalUtils.java | 590 long totalBases = 0; in scatterContigIntervals() local
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/ |
| H A D | AnalyzeSaturationMutagenesis.java | 578 final long totalBases = totalBaseCalls; in writeReadCounts() local
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