Updated the merging/consensus calling module.

fritzsedlazeck · Oct 4, 2016 · cf22614 · cf22614
1 parent c13a4cd
commit cf22614
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Showing 59 changed files with 307 additions and 366 deletions.
diff --git a/Debug/src/CorrectAllele.d b/Debug/src/CorrectAllele.d
diff --git a/Debug/src/CorrectAllele.o b/Debug/src/CorrectAllele.o
diff --git a/Debug/src/DetectDif.d b/Debug/src/DetectDif.d
diff --git a/Debug/src/DetectDif.o b/Debug/src/DetectDif.o
diff --git a/Debug/src/Extract_Seq.d b/Debug/src/Extract_Seq.d
diff --git a/Debug/src/Extract_Seq.o b/Debug/src/Extract_Seq.o
diff --git a/Debug/src/SURVIVOR.d b/Debug/src/SURVIVOR.d
diff --git a/Debug/src/SURVIVOR.o b/Debug/src/SURVIVOR.o
diff --git a/Debug/src/Summarize_SV.d b/Debug/src/Summarize_SV.d
diff --git a/Debug/src/Summarize_SV.o b/Debug/src/Summarize_SV.o
diff --git a/Debug/src/convert/ConvertMQ0Bed.d b/Debug/src/convert/ConvertMQ0Bed.d
diff --git a/Debug/src/convert/ConvertMQ0Bed.o b/Debug/src/convert/ConvertMQ0Bed.o
diff --git a/Debug/src/convert/Convert_Assemblytics.d b/Debug/src/convert/Convert_Assemblytics.d
diff --git a/Debug/src/convert/Convert_Assemblytics.o b/Debug/src/convert/Convert_Assemblytics.o
diff --git a/Debug/src/convert/Convert_Bionano.d b/Debug/src/convert/Convert_Bionano.d
diff --git a/Debug/src/convert/Convert_Bionano.o b/Debug/src/convert/Convert_Bionano.o
diff --git a/Debug/src/convert/Convert_Honey_tails.d b/Debug/src/convert/Convert_Honey_tails.d
diff --git a/Debug/src/convert/Convert_Honey_tails.o b/Debug/src/convert/Convert_Honey_tails.o
diff --git a/Debug/src/convert/Convert_Pindel.d b/Debug/src/convert/Convert_Pindel.d
diff --git a/Debug/src/convert/Convert_Pindel.o b/Debug/src/convert/Convert_Pindel.o
diff --git a/Debug/src/convert/Convert_VCF_to_BED.d b/Debug/src/convert/Convert_VCF_to_BED.d
diff --git a/Debug/src/convert/Convert_VCF_to_BED.o b/Debug/src/convert/Convert_VCF_to_BED.o
diff --git a/Debug/src/convert/Process_Lumpy.d b/Debug/src/convert/Process_Lumpy.d
diff --git a/Debug/src/convert/Process_Lumpy.o b/Debug/src/convert/Process_Lumpy.o
diff --git a/Debug/src/merge_vcf/IntervallTree.d b/Debug/src/merge_vcf/IntervallTree.d
diff --git a/Debug/src/merge_vcf/IntervallTree.o b/Debug/src/merge_vcf/IntervallTree.o
diff --git a/Debug/src/merge_vcf/combine_svs.d b/Debug/src/merge_vcf/combine_svs.d
diff --git a/Debug/src/merge_vcf/combine_svs.o b/Debug/src/merge_vcf/combine_svs.o
diff --git a/Debug/src/simulator/Eval_vcf.d b/Debug/src/simulator/Eval_vcf.d
diff --git a/Debug/src/simulator/Eval_vcf.o b/Debug/src/simulator/Eval_vcf.o
diff --git a/Debug/src/simulator/Pac_Simulator.d b/Debug/src/simulator/Pac_Simulator.d
diff --git a/Debug/src/simulator/Pac_Simulator.o b/Debug/src/simulator/Pac_Simulator.o
diff --git a/Debug/src/simulator/SV_Simulator.d b/Debug/src/simulator/SV_Simulator.d
diff --git a/Debug/src/simulator/SV_Simulator.o b/Debug/src/simulator/SV_Simulator.o
diff --git a/Debug/src/vcfs/Annotate_vcf.d b/Debug/src/vcfs/Annotate_vcf.d
diff --git a/Debug/src/vcfs/Annotate_vcf.o b/Debug/src/vcfs/Annotate_vcf.o
diff --git a/Debug/src/vcfs/Combine_3_VCF.d b/Debug/src/vcfs/Combine_3_VCF.d
diff --git a/Debug/src/vcfs/Combine_3_VCF.o b/Debug/src/vcfs/Combine_3_VCF.o
diff --git a/Debug/src/vcfs/Compoverlap_VCF.d b/Debug/src/vcfs/Compoverlap_VCF.d
diff --git a/Debug/src/vcfs/Compoverlap_VCF.o b/Debug/src/vcfs/Compoverlap_VCF.o
diff --git a/Debug/src/vcfs/Filter_vcf.d b/Debug/src/vcfs/Filter_vcf.d
diff --git a/Debug/src/vcfs/Filter_vcf.o b/Debug/src/vcfs/Filter_vcf.o
diff --git a/Debug/src/vcfs/Merge_VCF.d b/Debug/src/vcfs/Merge_VCF.d
diff --git a/Debug/src/vcfs/Merge_VCF.o b/Debug/src/vcfs/Merge_VCF.o
diff --git a/INSTALL b/INSTALL
@@ -2,6 +2,6 @@ change in the Debug directory.
 type:
 	make
 
-you should find an executable in the same director.
+you should find an executable in the same directory.
 If you have problems please let me know:
-fritz.sedlazeck@gmail.cohould find an executable in the same director.
+fritz.sedlazeck@gmail.com
diff --git a/README.md b/README.md
@@ -24,18 +24,20 @@ to see the individual parameters for each option.
 
 choose the ID from these options:
 ```
+Possible options
 1: Simulate SV on genome
 2: Simulate PacBio reads
 3: Evaluate SV calling
 4: Merge SV calls (vcf) 
-5: Consensus call from 2/3 callers
+5: Merge + Consensus call from different callers/vcf files
 6: Extract genes influenced by SVs
 7: Filter and convert SV calls from Delly
 8: Filter and convert SV calls from Lumpy
 9: Filter and convert SV calls from Pindel
-10: Convert SV calls from Assemblytics
-11: Summarize MQ 0 coverage to bed file
-12: Summarize SVs events in VCF file
+10: Convert SV calls from PBHoney (tails)
+11: Convert SV calls from Assemblytics
+12: Summarize MQ 0 coverage to bed file
+13: Summarize SVs events in VCF file
 ```
 
 **************************************

diff --git a/src/SURVIVOR.cpp b/src/SURVIVOR.cpp
@@ -81,7 +81,7 @@ int main(int argc, char *argv[]) {
 				std::cerr << "Output vcf file" << std::endl;
 			}
 			break;
-		case 5:
+		/*case 5:
 			if (argc == 7) {
 				//merge 3 SV calls from the same strain
 				combine_calls(std::string(argv[2]), std::string(argv[3]), std::string(argv[4]), atoi(argv[5]), std::string(argv[6]));
@@ -92,7 +92,7 @@ int main(int argc, char *argv[]) {
 				std::cerr << "max dist" << std::endl;
 				std::cerr << "Output prefix" << std::endl;
 			}
-			break;
+			break;*/
 		case 6:
 			if (argc == 6) {
 				generate_gene_list(std::string(argv[2]), std::string(argv[3]), atoi(argv[4]), std::string(argv[5]));
@@ -180,20 +180,21 @@ int main(int argc, char *argv[]) {
 			}
 			break;
 
-		case 14:
-			if (argc == 7) {
+		case 5: //prev 14!
+			if (argc == 8) {
 				//merge 3 SV calls from the same strain
 			//	combine_calls_new(std::string(argv[2]), atoi(argv[3]), atoi(argv[4]), std::string(argv[5]));
-				combine_calls_svs(std::string(argv[2]), atoi(argv[3]), atoi(argv[4]), atoi(argv[5]), std::string(argv[6]));
+				combine_calls_svs(std::string(argv[2]), atoi(argv[3]), atoi(argv[4]), atoi(argv[5]), atoi(argv[6]), std::string(argv[7]));
 			} else {
 				std::cerr << "Tab file with names" << std::endl;
 				std::cerr << "max distance between breakpoints" << std::endl;
 				std::cerr << "Minimum number of supporting caller" << std::endl;
 				std::cerr << "Take the type into account (1==yes, else no)"<<std::endl;
+				std::cerr << "Take the strands of SVs into account (1==yes, else no)"<<std::endl;
 				std::cerr << "Output prefix" << std::endl;
 			}
 			break;
-		case 15:
+		/*case 15:
 			if (argc == 5) {
 				//eval calls paper
 				eval_paper(std::string(argv[2]), std::string(argv[3]), atoi(argv[4]));
@@ -211,7 +212,7 @@ int main(int argc, char *argv[]) {
 				std::cerr << "*.smap file" << std::endl;
 				std::cerr << "output file" << std::endl;
 			}
-			break;
+			break;*/
 		default:
 			break;
 		}
@@ -230,7 +231,7 @@ int main(int argc, char *argv[]) {
 		std::cerr << "11: Convert SV calls from Assemblytics" << std::endl;
 		std::cerr << "12: Summarize MQ 0 coverage to bed file" << std::endl;
 		std::cerr << "13: Summarize SVs events in VCF file" << std::endl;
-		std::cerr << "14: Combine calls from different vcf files" << std::endl;
+	//	std::cerr << "14: Combine calls from different vcf files" << std::endl;
 	}
 	return 0;
 }