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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,26 +1,3 @@ | ||
| /* | ||
| ============================================================================ | ||
| SV VCF properties | ||
| ============================================================================ | ||
| Copyright (C) 2015 Tobias Rausch | ||
| This program is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU General Public License as published by | ||
| the Free Software Foundation, either version 3 of the License, or | ||
| any later version. | ||
| This program is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| GNU General Public License for more details. | ||
| You should have received a copy of the GNU General Public License | ||
| along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| ============================================================================ | ||
| Contact: Tobias Rausch ([email protected]) | ||
| ============================================================================ | ||
| */ | ||
|
|
||
| #include <iostream> | ||
| #include <set> | ||
| #include <vector> | ||
|
|
@@ -122,8 +99,8 @@ int main(int argc, char **argv) { | |
| float* fic = NULL; | ||
| int32_t nce = 0; | ||
| float* ce = NULL; | ||
| int32_t nrsq = 0; | ||
| float* rsq = NULL; | ||
| int32_t nexchet = 0; | ||
| float* exchet = NULL; | ||
| int32_t nhwepval = 0; | ||
| float* hwepval = NULL; | ||
| int32_t nchr2 = 0; | ||
|
|
@@ -174,8 +151,8 @@ int main(int argc, char **argv) { | |
| if (_isKeyPresent(hdr, "HOMLEN")) cMap["homlen"] = fieldIndex++; | ||
| if (_isKeyPresent(hdr, "FIC")) cMap["fic"] = fieldIndex++; | ||
| if (_isKeyPresent(hdr, "CE")) cMap["ce"] = fieldIndex++; | ||
| if (_isKeyPresent(hdr, "RSQ")) cMap["rsq"] = fieldIndex++; | ||
| if (_isKeyPresent(hdr, "HWEpval")) cMap["hwepval"] = fieldIndex++; | ||
| if (_isKeyPresent(hdr, "ExcHet")) cMap["exchet"] = fieldIndex++; | ||
| if (_isKeyPresent(hdr, "HWE")) cMap["hwepval"] = fieldIndex++; | ||
| if (_isKeyPresent(hdr, "GQ")) { | ||
| cMap["refgq"] = fieldIndex++; | ||
| cMap["altgq"] = fieldIndex++; | ||
|
|
@@ -216,7 +193,7 @@ int main(int argc, char **argv) { | |
| bool rcPresent = false; | ||
| bool dvPresent = false; | ||
| bool ficPresent = false; | ||
| bool rsqPresent = false; | ||
| bool exchetPresent = false; | ||
| bool hwePresent = false; | ||
| bool ciPresent = false; | ||
| bool svtPresent = false; | ||
|
|
@@ -247,11 +224,11 @@ int main(int argc, char **argv) { | |
| if (bcf_get_info_float(hdr, rec, "FIC", &fic, &nfic) > 0) ficPresent = true; | ||
| } | ||
| if (_isKeyPresent(hdr, "CE")) bcf_get_info_float(hdr, rec, "CE", &ce, &nce); | ||
| if (_isKeyPresent(hdr, "RSQ")) { | ||
| if (bcf_get_info_float(hdr, rec, "RSQ", &rsq, &nrsq) > 0) rsqPresent = true; | ||
| if (_isKeyPresent(hdr, "ExcHet")) { | ||
| if (bcf_get_info_float(hdr, rec, "ExcHet", &exchet, &nexchet) > 0) exchetPresent = true; | ||
| } | ||
| if (_isKeyPresent(hdr, "HWEpval")) { | ||
| if (bcf_get_info_float(hdr, rec, "HWEpval", &hwepval, &nhwepval) > 0) hwePresent = true; | ||
| if (_isKeyPresent(hdr, "HWE")) { | ||
| if (bcf_get_info_float(hdr, rec, "HWE", &hwepval, &nhwepval) > 0) hwePresent = true; | ||
| } | ||
| if (_isKeyPresent(hdr, "SVTYPE")) { | ||
| if (bcf_get_info_string(hdr, rec, "SVTYPE", &svt, &nsvt) > 0) svtPresent = true; | ||
|
|
@@ -312,13 +289,18 @@ int main(int argc, char **argv) { | |
| int32_t uncalled = 0; | ||
| for (int i = 0; i < bcf_hdr_nsamples(hdr); ++i) { | ||
| if ((bcf_gt_allele(gt[i*2]) != -1) && (bcf_gt_allele(gt[i*2 + 1]) != -1)) { | ||
| int gt_type = bcf_gt_allele(gt[i*2]) + bcf_gt_allele(gt[i*2 + 1]); | ||
| ++ac[bcf_gt_allele(gt[i*2])]; | ||
| ++ac[bcf_gt_allele(gt[i*2 + 1])]; | ||
| if (dvPresent) { | ||
| if (rr[i] + rv[i] + dr[i] + dv[i] == 0) { | ||
| // Imputed GT | ||
| ++uncalled; | ||
| continue; | ||
| } | ||
| if (precise) supportsum += rr[i] + rv[i]; | ||
| else supportsum += dr[i] + dv[i]; | ||
| } | ||
| int gt_type = bcf_gt_allele(gt[i*2]) + bcf_gt_allele(gt[i*2 + 1]); | ||
| ++ac[bcf_gt_allele(gt[i*2])]; | ||
| ++ac[bcf_gt_allele(gt[i*2 + 1])]; | ||
|
|
||
| if (gt_type == 0) { | ||
| // Non-carrier | ||
|
|
@@ -339,8 +321,9 @@ int main(int argc, char **argv) { | |
| } else gqRef.push_back(0); | ||
| if (rcPresent) { | ||
| rcRef.push_back( rc[i] ); | ||
| if (_isKeyPresent(hdr, "RCL")) rcRefRatio.push_back( (double) rc[i] / (double) (rcl[i] + rcr[i]) ); | ||
| else rcRefRatio.push_back((double) rc[i]); | ||
| if (_isKeyPresent(hdr, "RCL")) { | ||
| if ((rcl[i] + rcr[i]) > 0) rcRefRatio.push_back( 2.0 * (double) rc[i] / (double) (rcl[i] + rcr[i]) ); | ||
| } else rcRefRatio.push_back((double) rc[i]); | ||
| } | ||
| if (dvPresent) { | ||
| if (precise) ratioRef.push_back( (double) rv[i] / (double) (rr[i] + rv[i]) ); | ||
|
|
@@ -372,8 +355,9 @@ int main(int argc, char **argv) { | |
| } | ||
| } else gqAlt.push_back(0); | ||
| if (rcPresent) { | ||
| if (_isKeyPresent(hdr, "RCL")) rcAltRatio.push_back( (double) rc[i] / (double) (rcl[i] + rcr[i]) ); | ||
| else rcAltRatio.push_back((double) rc[i]); | ||
| if (_isKeyPresent(hdr, "RCL")) { | ||
| if ((rcl[i] + rcr[i]) > 0) rcAltRatio.push_back( 2.0 * (double) rc[i] / (double) (rcl[i] + rcr[i]) ); | ||
| } else rcAltRatio.push_back((double) rc[i]); | ||
| } | ||
| if (dvPresent) { | ||
| if (precise) ratioAlt.push_back( (double) rv[i] / (double) (rr[i] + rv[i]) ); | ||
|
|
@@ -385,7 +369,8 @@ int main(int argc, char **argv) { | |
| } | ||
| std::string rareCarrier = "NA"; | ||
| if (rareCarrierSet.size() == 1) rareCarrier = *(rareCarrierSet.begin()); | ||
| TPrecision af = (TPrecision) ac[1] / (TPrecision) (ac[0] + ac[1]); | ||
| TPrecision af = 0; | ||
| if ((ac[0] + ac[1]) > 0) af = (TPrecision) ac[1] / (TPrecision) (ac[0] + ac[1]); | ||
| int32_t svlen = 1; | ||
| if ((svt != NULL) && (std::string(svt) == "BND")) svlen = 0; | ||
| else if (endsv != 0) svlen = endsv - rec->pos; | ||
|
|
@@ -463,8 +448,8 @@ int main(int argc, char **argv) { | |
| if ((precise) && (nce > 0)) std::cout << *ce; | ||
| else std::cout << "0"; | ||
| } | ||
| else if (*cHead == "rsq") { | ||
| if (rsqPresent) std::cout << *rsq; | ||
| else if (*cHead == "exchet") { | ||
| if (exchetPresent) std::cout << *exchet; | ||
| else std::cout << "NA"; | ||
| } else if (*cHead == "hwepval") { | ||
| if (hwePresent) std::cout << *hwepval; | ||
|
|
@@ -483,7 +468,7 @@ int main(int argc, char **argv) { | |
| if (svt != NULL) free(svt); | ||
| if (fic != NULL) free(fic); | ||
| if (ce != NULL) free(ce); | ||
| if (rsq != NULL) free(rsq); | ||
| if (exchet != NULL) free(exchet); | ||
| if (hwepval != NULL) free(hwepval); | ||
| if (chr2 != NULL) free(chr2); | ||
| if (ct != NULL) free(ct); | ||
|
|
||