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Searched refs:rsID (Results 1 – 9 of 9) sorted by relevance

/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/annotator/
H A DVariantOverlapAnnotator.java76 final String rsID = getRsID(vcsAtLoc, vcToAnnotate); in annotateRsID() local
79 if ( rsID != null ) { in annotateRsID()
83 return vcb.id(rsID).make(); in annotateRsID()
84 } else if ( ! vcToAnnotate.getID().contains(rsID) ) { in annotateRsID()
85 return vcb.id(vcToAnnotate.getID() + VCFConstants.ID_FIELD_SEPARATOR + rsID).make(); in annotateRsID()
/dports/biology/bolt-lmm/BOLT-LMM_v2.3.4/src/
H A DSnpData.cpp357 string rsID; iss >> rsID; in processSnps() local
358 if (rsID_to_ind.find(rsID) == rsID_to_ind.end()) { in processSnps()
363 else if (snpVCnum[rsID_to_ind[rsID]] != excludeVCnum) { in processSnps()
364 snpVCnum[rsID_to_ind[rsID]] = excludeVCnum; in processSnps()
390 string rsID; iss >> rsID; in processSnps() local
391 if (rsID_to_ind.find(rsID) == rsID_to_ind.end()) { in processSnps()
396 else if (snpVCnum[rsID_to_ind[rsID]] == excludeVCnum) { in processSnps()
398 cerr << "WARNING: SNP has been excluded: " << rsID << endl; in processSnps()
401 else if (snpVCnum[rsID_to_ind[rsID]] == nonGrmVCnum) { in processSnps()
410 cerr << "ERROR: SNP " << rsID << " is assigned to VC '" << vcName in processSnps()
[all …]
H A DFileUtils.cpp303 char snpID[65536], rsID[65536], chrStr[65536], allele1[65536], allele0[65536]; in checkBgenSample() local
308 fread(rsID, 1, LR, fin); rsID[LR] = '\0'; cout << "first rsID: " << string(rsID) << endl; in checkBgenSample()
311 string snpName = string(rsID)=="." ? snpID : rsID; in checkBgenSample()
H A DBolt.cpp2525 string chromStr, rsID; double genpos; int physpos; in streamDosage2() local
2526 issMapLine >> chromStr >> rsID >> genpos >> physpos; in streamDosage2()
2532 if (snpID != rsID) { in streamDosage2()
2605 string snpID, rsID, allele1, allele0; int physpos; in streamImpute2() local
2720 char /**snpID,*/ *rsID, *allele1, *allele0; in fastStreamImpute2() local
2875 char snpID[65536], rsID[65536], chrStr[65536]; in streamBgen() local
2892 …fread(rsID, 1, LR, fin); rsID[LR] = '\0'; // cout << "rsID: " << string(rsID) << " " << std::flush; in streamBgen()
2948 string snpName = string(rsID)=="." ? snpID : rsID; in streamBgen()
3212 char snpID[65536], rsID[65536], chrStr[65536]; in streamBgen2() local
3234 …fread(rsID, 1, LR, fin); rsID[LR] = '\0'; // cout << "rsID: " << string(rsID) << " " << std::flush; in streamBgen2()
[all …]
H A DBoltParams.cpp547 string rsID; iss >> rsID; in processCommandLineArgs() local
635 string snpID, rsID; iss >> snpID >> rsID; in processCommandLineArgs() local
/dports/biology/gatk/gatk-4.2.0.0/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/
H A DValidateVariants.java300 for (VariantContext rsID : featureContext.getValues(dbsnp.dbsnp)) { in getRSIDs()
301 rsIDs.addAll(Arrays.asList(rsID.getID().split(VCFConstants.ID_FIELD_SEPARATOR))); in getRSIDs()
/dports/net-mgmt/librenms/librenms-21.5.1/mibs/arraynetworks/
H A DCA-SNMP-MIB8453 rsID DisplayString,
473 rsID OBJECT-TYPE
/dports/biology/hisat2/hisat2-2.2.1/
H A DMANUAL1208 …_positions/ALL.chr22.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_db…
/dports/biology/hisat2/hisat2-2.2.1/docs/_pages/
H A Dmanual.md1272 …_positions/ALL.chr22.phase3_shapeit2_mvncall_integrated_v3plus_nounphased.rsID.genotypes.GRCh38_db…