modified: TIDDIT.py

	modified:   src/TIDDIT.cpp
	modified:   src/TIDDIT_filtering.py
	modified:   src/TIDDIT_signals.py

TIDDIT.py

@@ -7,7 +7,7 @@
 sys.path.insert(0, '{}/src/'.format(wd))
 import TIDDIT_calling
 
-version = "2.3.0"
+version = "2.3.1"
 parser = argparse.ArgumentParser("""TIDDIT-{}""".format(version),add_help=False)
 parser.add_argument('--sv'       , help="call structural variation", required=False, action="store_true")
 parser.add_argument('--cov'        , help="generate a coverage bed file", required=False, action="store_true")

src/TIDDIT.cpp

@@ -45,7 +45,7 @@ int main(int argc, char **argv) {
 	int min_variant_size= 100;
 	int sample = 100000000;
 	string outputFileHeader ="output";
-	string version = "2.3.0";
+	string version = "2.3.1";
 
 	//collect all options as a vector
 	vector<string> arguments(argv, argv + argc);

src/TIDDIT_filtering.py

@@ -113,22 +113,22 @@ def fetch_variant_type(chrA,chrB,candidate,args,library_stats):
 					var="<DEL>"		
 
 	if candidate["discs"]:
-		if candidate["e2"]*1.6 <= (candidate["discs"]):
+		if candidate["e2"]*1.5 <= (candidate["discs"]):
 			GT="1/1"
 		else:
 			GT="0/1"
 	else:
-		if candidate["e2"]*1.6 <= (candidate["splits"]):
+		if candidate["e2"]*1.5 <= (candidate["splits"]):
 			GT="1/1"
 		else:
 			GT="0/1"
 
-	if "DUP" in var or var == "<DEL>":
-		if var == "DEL" and candidate["covM"]/library_stats["chr_cov"][chrA] < 0.1:
+	if ("DUP" in var or var == "<DEL>") and library_stats["chr_cov"][chrA] != 0:
+		if var == "<DEL>" and candidate["covM"]/library_stats["chr_cov"][chrA] < 0.1:
 			GT="1/1"
-		elif var == "DUP" and candidate["covM"]/library_stats["chr_cov"][chrA] > 1.8: 
+		elif "DUP" in var and candidate["covM"]/library_stats["chr_cov"][chrA] > 1.8: 
 			GT="1/1"
- 
+
 	return(var,variant_type,GT)
 
 def Part(a, b, sizeA, sizeB, gap, insert_mean, insert_stddev, coverage, readLength ):

src/TIDDIT_signals.py

@@ -126,8 +126,14 @@ def signals(args,coverage_data):
 			idx_a=len(coverage_data[chrA])-1
 		coverage_data[chrA][idx_a,2]+=1
 
+
 	if len(signal_data):
 		args.c.executemany('INSERT INTO TIDDITcall VALUES (?,?,?,?,?,?,?,?,?,?,?,?)',signal_data)  
+
+	#If no signals were found, parse and return the header
+	if first_signal:
+		chromosomes,library_stats,chromosome_len=find_contigs(header)
+
 	return(header,chromosomes,library_stats)
 
 #analyse the cigar operation of the read