From de309ee16ede58db88df6b5c1a89f0b8f0194449 Mon Sep 17 00:00:00 2001
From: Maximilian Stammnitz <MaximilianStammnitz@users.noreply.github.com>
Date: Tue, 11 Aug 2020 16:27:14 +0100
Subject: [PATCH] Update sv.py

Don't remove INV calls from Manta v1.4.0 during merging.
---
 sv.py | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/sv.py b/sv.py
index 7d191ef..2c10999 100644
--- a/sv.py
+++ b/sv.py
@@ -43,9 +43,8 @@ def __init__(self, vcf_record, check_type = True, join_mode = False, output_ids
             if info_dict["SVTYPE"] == "DEL_ALU" or info_dict["SVTYPE"] == "DEL_LINE1":
                 info_dict["SVTYPE"] = "DEL"
             elif info_dict["SVTYPE"] == "ALU" or info_dict["SVTYPE"] == "LINE1" or info_dict["SVTYPE"] == "SVA" or \
-                 info_dict["SVTYPE"] == "DUP" or info_dict["SVTYPE"] == "CNV" or info_dict["SVTYPE"] == "INVDUP" or \
-                 info_dict["SVTYPE"] == "INV":
-                info_dict["SVTYPE"] = "INS"
+                 info_dict["SVTYPE"] == "DUP" or info_dict["SVTYPE"] == "CNV" or info_dict["SVTYPE"] == "INVDUP":
+                  info_dict["SVTYPE"] = "INS"
             elif info_dict["SVTYPE"] == "TRA":
                 info_dict["SVTYPE"] = "BND"