Merge pull request #71 from Meltpinkg/master

Fix a bug that will report the fake SV. ref #64

src/cuteSV/cuteSV

@@ -493,8 +493,7 @@ def parse_read(read, Chr_name, SV_size, min_mapq, max_split_parts, min_read_len,
 			if element[0] in [0, 2, 7, 8]:
 				shift_ins += element[1]
 			if element[0] == 1 and element[1] >= SV_size:
-				shift_ins += 1
-				Combine_sig_in_same_read_ins.append([pos_start+shift_ins-1, element[1],
+				Combine_sig_in_same_read_ins.append([pos_start+shift_ins, element[1],
 					str(read.query_sequence[shift_ins_read-element[1]-hardclip_left:shift_ins_read-hardclip_left])])
 
 

src/cuteSV/cuteSV_resolveDUP.py

@@ -48,7 +48,11 @@ def resolution_DUP(path, chr, read_count, max_cluster_bias, sv_size,
 			semi_dup_cluster = []
 			semi_dup_cluster.append([pos_1, pos_2, read_id])
 		else:
-			semi_dup_cluster.append([pos_1, pos_2, read_id])
+			if semi_dup_cluster[-1][0] == semi_dup_cluster[-1][1] == 0:
+				semi_dup_cluster = []
+				semi_dup_cluster.append([pos_1, pos_2, read_id])
+			else:
+				semi_dup_cluster.append([pos_1, pos_2, read_id])
 
 	if len(semi_dup_cluster) >= read_count:
 		if semi_dup_cluster[-1][0] == semi_dup_cluster[-1][1] == 0:

src/cuteSV/cuteSV_resolveINDEL.py

@@ -77,7 +77,11 @@ def resolution_DEL(path, chr, svtype, read_count, threshold_gloab, max_cluster_b
 			semi_del_cluster = []
 			semi_del_cluster.append([pos, indel_len, read_id])
 		else:
-			semi_del_cluster.append([pos, indel_len, read_id])
+			if semi_del_cluster[-1][0] == semi_del_cluster[-1][1] == 0:
+				semi_del_cluster = []
+				semi_del_cluster.append([pos, indel_len, read_id])
+			else:
+				semi_del_cluster.append([pos, indel_len, read_id])
 
 	if len(semi_del_cluster) >= read_count:
 		if semi_del_cluster[-1][0] == semi_del_cluster[-1][1] == 0:
@@ -256,7 +260,11 @@ def resolution_INS(path, chr, svtype, read_count, threshold_gloab,
 			semi_ins_cluster = []
 			semi_ins_cluster.append([pos, indel_len, read_id, ins_seq])
 		else:
-			semi_ins_cluster.append([pos, indel_len, read_id, ins_seq])
+			if semi_ins_cluster[-1][0] == semi_ins_cluster[-1][1] == 0:
+				semi_ins_cluster = []
+				semi_ins_cluster.append([pos, indel_len, read_id, ins_seq])
+			else:
+				semi_ins_cluster.append([pos, indel_len, read_id, ins_seq])
 
 	if len(semi_ins_cluster) >= read_count:
 		if semi_ins_cluster[-1][0] == semi_ins_cluster[-1][1] == 0:

src/cuteSV/cuteSV_resolveINV.py

@@ -69,7 +69,11 @@ def resolution_INV(path, chr, svtype, read_count, max_cluster_bias, sv_size,
 			semi_inv_cluster = []
 			semi_inv_cluster.append([breakpoint_1_in_read, breakpoint_2_in_read, read_id, strand])
 		else:
-			semi_inv_cluster.append([breakpoint_1_in_read, breakpoint_2_in_read, read_id, strand])
+			if semi_inv_cluster[-1][0] == semi_inv_cluster[-1][1] == 0:
+				semi_inv_cluster = []
+				semi_inv_cluster.append([breakpoint_1_in_read, breakpoint_2_in_read, read_id, strand])
+			else:
+				semi_inv_cluster.append([breakpoint_1_in_read, breakpoint_2_in_read, read_id, strand])
 
 	if len(semi_inv_cluster) >= read_count:
 		if semi_inv_cluster[-1][0] == semi_inv_cluster[-1][1] == 0:

src/cuteSV/cuteSV_resolveTRA.py

@@ -62,7 +62,11 @@ def resolution_TRA(path, chr_1, chr_2, read_count, overlap_size, max_cluster_bia
 			semi_tra_cluster = []
 			semi_tra_cluster.append([pos_1, pos_2, read_id, BND_type])
 		else:
-			semi_tra_cluster.append([pos_1, pos_2, read_id, BND_type])
+			if semi_tra_cluster[-1][0] == semi_tra_cluster[-1][1] == 0:
+				semi_tra_cluster = []
+				semi_tra_cluster.append([pos_1, pos_2, read_id, BND_type])
+			else:
+				semi_tra_cluster.append([pos_1, pos_2, read_id, BND_type])
 
 	if len(semi_tra_cluster) >= read_count:
 		if semi_tra_cluster[-1][0] == semi_tra_cluster[-1][1] == 0: