| /dports/biology/mothur/mothur-1.46.1/source/chimera/ |
| H A D | slayer.h | 19 struct snps { struct
20 char queryChar;
21 char parentAChar;
22 char parentBChar;
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| /dports/biology/bolt-lmm/BOLT-LMM_v2.3.4/src/ |
| H A D | LDscoreCalibration.cpp | 62 vector <bool> removeOutlierWindows in removeOutlierWindows()
190 pair <double, double> calibrateStatPair in calibrateStatPair()
241 RegressionInfo calibrateStat in calibrateStat()
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| H A D | SnpData.hpp | 57 std::vector <SnpInfo> snps; // [VECTOR]: M member in LMM::SnpData
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| H A D | PhenoBuilder.cpp | 112 const vector <SnpInfo> &snps = bolt.getSnpData().getSnpInfo(); in genPhenoCausal() local
215 const vector <SnpInfo> &snps = bolt.getSnpData().getSnpInfo(); in genPhenoCausalRegions() local
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| H A D | BoltMain.cpp | 136 const vector <SnpInfo> &snps = snpData.getSnpInfo(); in main() local
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| /dports/biology/stacks/stacks-2.4/src/ |
| H A D | mstack.h | 56 vector<SNP *> snps; // Single Nucleotide Polymorphisms found in this Stack variable
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| H A D | locus.h | 84 vector<SNP *> snps; // Single Nucleotide Polymorphisms in this stack. variable
104 delete snps[i]; in ~Locus() local
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| H A D | locus.cc | 202 vector<SNP *> snps; in adjust_and_add_snps_for_gaps() local
255 vector<SNP *> snps; in remove_snps_from_gaps() local
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| H A D | stacks.h | 250 vector<SNP *> snps; variable
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| H A D | phasedstacks.cc | 366 map<int, int> buckets, snps; in four_gamete_test() local
480 map<int, int> buckets, snps; in dprime_blocks() local
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| /dports/biology/mummer/mummer-4.0.0beta2-2-g277dac5/src/tigr/ |
| H A D | show-snps.cc | 201 vector<const SNP_t *> snps; in main() local
707 void PrintHuman (const vector<const SNP_t *> & snps, in PrintHuman()
787 void PrintTabular (const vector<const SNP_t *> & snps, in PrintTabular()
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| /dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/utils/variant/ |
| H A D | DbSnpBitSetUtil.java | 23 public DbSnpBitSetUtil snps; field in DbSnpBitSetUtil.DbSnpBitSets
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| /dports/biology/snpeff/snpEff/scripts/ |
| H A D | ped2vcf.py | 60 snps = [] variable
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| /dports/biology/hisat2/hisat2-2.2.1/ |
| H A D | repeat_builder.h | 432 EList<SeedSNP *> snps; variable
529 EList<SeedSNP *>& snps() { return snps_; } in snps() function
530 const EList<SeedSNP *>& snps() const { return snps_; } in snps() function
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| H A D | hisat2_simulate_reads.py | 200 def sanity_check_input(genome_seq, genes, transcripts, snps, frag_len): argument
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| /dports/biology/gatk/gatk-4.2.0.0/scripts/cnn_variant_wdl/ |
| H A D | vcf_analysis.R | 101 snps <- subset(d, EVENTLENGTH == 0) globalVar
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| H A D | vcf_analysis_no_truth.R | 98 snps <- subset(d, EVENTLENGTH == 0) globalVar
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| /dports/biology/artemis/artemis-17.0.1-11-g3e43d27e/uk/ac/sanger/artemis/components/alignment/ |
| H A D | BamView.java | 1464 List<Integer> snps = getSNPs(samRecord); in drawLineView() local
1602 List<Integer> snps = getSNPs(samRecord); in drawStackView() local
1708 List<Integer> snps = getSNPs(samRecord); in drawStrand() local
2029 float pixPerBase, int baseAtStartOfView, int scaleHeight, List<Integer> snps, int ydiff) in drawLoneRead()
2191 final List<Integer> snps, in drawRead()
2381 private void showSNPsOnReads(final List<Integer> snps, in showSNPsOnReads()
2411 ArrayList<Integer> snps = null; in getSNPs() local
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| H A D | LookSeqPanel.java | 169 final JCheckBoxMenuItem snps = in setUpPopupMenu() local
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| /dports/biology/vcflib/vcflib-1.0.2/src/ |
| H A D | vcfstats.cpp | 230 int snps = 0; in main() local
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
| H A D | vcfstats.cpp | 218 int snps = 0; in main() local
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
| H A D | vcfstats.cpp | 218 int snps = 0; in main() local
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| /dports/biology/hisat2/hisat2-2.2.1/evaluation/real/ |
| H A D | calculate_read_cost.py | 437 def check_snps(snps, check_type, ref_pos, read_seq): argument
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| /dports/biology/emboss/EMBOSS-6.6.0/emboss/ |
| H A D | diffseq.c | 288 ajint snps = 0; in diffseq_Diff() local
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| /dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/mason2/ |
| H A D | genomic_variants.h | 259 seqan::String<SnpRecord> snps; member
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