| /dports/biology/vcflib/vcflib-1.0.2/src/ |
| H A D | gl-XPEHH.cpp | 335 int indIndex = 0; in loadPhased() local
337 string g = pos->genotypes[indIndex]; in loadPhased()
339 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
340 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
341 indIndex++; in loadPhased()
373 int indIndex = 0; in localPhase() local
376 int g = pos->geno_index[indIndex]; in localPhase()
378 if(rang < pos->unphred_p[indIndex][0]){ in localPhase()
392 tempHaplotypes[indIndex][0].append("1"); in localPhase()
393 tempHaplotypes[indIndex][1].append("1"); in localPhase()
[all …]
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| H A D | plotHaps.cpp | 151 int indIndex = 0; in loadPhased() local
156 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
157 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
158 indIndex += 1; in loadPhased()
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| H A D | vcfld.cpp | 137 int indIndex = 0; in loadPhased() local
142 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
143 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
144 indIndex += 1; in loadPhased()
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| H A D | sequenceDiversity.cpp | 161 int indIndex = 0; in loadPhased() local
166 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
167 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
168 indIndex += 1; in loadPhased()
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| H A D | vcfToHap.cpp | 187 int indIndex = 0; in loadPhased() local
192 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
193 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
194 indIndex += 1; in loadPhased()
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| H A D | xpEHH.cpp | 192 int indIndex = 0; in loadPhased() local
197 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
198 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
199 indIndex += 1; in loadPhased()
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| H A D | iHS.cpp | 408 int indIndex = 0; in loadPhased() local
413 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
414 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
415 indIndex += 1; in loadPhased()
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| H A D | hapLrt.cpp | 305 int indIndex = 0; in loadPhased() local
313 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
314 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
315 indIndex += 1; in loadPhased()
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib-temp/src/ |
| H A D | gl-XPEHH.cpp | 326 int indIndex = 0; in loadPhased() local
328 string g = pos->genotypes[indIndex]; in loadPhased()
330 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
331 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
332 indIndex++; in loadPhased()
364 int indIndex = 0; in localPhase() local
367 int g = pos->geno_index[indIndex]; in localPhase()
369 if(rang < pos->unphred_p[indIndex][0]){ in localPhase()
383 tempHaplotypes[indIndex][0].append("1"); in localPhase()
384 tempHaplotypes[indIndex][1].append("1"); in localPhase()
[all …]
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| H A D | plotHaps.cpp | 143 int indIndex = 0; in loadPhased() local
148 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
149 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
150 indIndex += 1; in loadPhased()
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| H A D | vcfld.cpp | 126 int indIndex = 0; in loadPhased() local
131 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
132 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
133 indIndex += 1; in loadPhased()
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| H A D | vcfToHap.cpp | 178 int indIndex = 0; in loadPhased() local
183 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
184 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
185 indIndex += 1; in loadPhased()
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| H A D | xpEHH.cpp | 183 int indIndex = 0; in loadPhased() local
188 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
189 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
190 indIndex += 1; in loadPhased()
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| H A D | sequenceDiversity.cpp | 151 int indIndex = 0; in loadPhased() local
156 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
157 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
158 indIndex += 1; in loadPhased()
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| H A D | hapLrt.cpp | 295 int indIndex = 0; in loadPhased() local
303 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
304 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
305 indIndex += 1; in loadPhased()
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| H A D | iHS.cpp | 394 int indIndex = 0; in loadPhased() local
399 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
400 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
401 indIndex += 1; in loadPhased()
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| H A D | meltEHH.cpp | 370 int indIndex = 0; in loadPhased() local
375 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
376 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
377 indIndex += 1; in loadPhased()
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| /dports/biology/freebayes/freebayes-1.3.5/vcflib/src/ |
| H A D | gl-XPEHH.cpp | 326 int indIndex = 0; in loadPhased() local
328 string g = pos->genotypes[indIndex]; in loadPhased()
330 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
331 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
332 indIndex++; in loadPhased()
364 int indIndex = 0; in localPhase() local
367 int g = pos->geno_index[indIndex]; in localPhase()
369 if(rang < pos->unphred_p[indIndex][0]){ in localPhase()
383 tempHaplotypes[indIndex][0].append("1"); in localPhase()
384 tempHaplotypes[indIndex][1].append("1"); in localPhase()
[all …]
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| H A D | plotHaps.cpp | 143 int indIndex = 0; in loadPhased() local
148 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
149 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
150 indIndex += 1; in loadPhased()
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| H A D | vcfld.cpp | 126 int indIndex = 0; in loadPhased() local
131 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
132 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
133 indIndex += 1; in loadPhased()
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| H A D | vcfToHap.cpp | 178 int indIndex = 0; in loadPhased() local
183 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
184 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
185 indIndex += 1; in loadPhased()
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| H A D | xpEHH.cpp | 183 int indIndex = 0; in loadPhased() local
188 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
189 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
190 indIndex += 1; in loadPhased()
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| H A D | sequenceDiversity.cpp | 151 int indIndex = 0; in loadPhased() local
156 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
157 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
158 indIndex += 1; in loadPhased()
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| H A D | hapLrt.cpp | 295 int indIndex = 0; in loadPhased() local
303 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
304 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
305 indIndex += 1; in loadPhased()
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| H A D | iHS.cpp | 394 int indIndex = 0; in loadPhased() local
399 haplotypes[indIndex][0].append(gs[0]); in loadPhased()
400 haplotypes[indIndex][1].append(gs[1]); in loadPhased()
401 indIndex += 1; in loadPhased()
|