flip pos, END where needed

see brentp/smoove#56
brentp · Feb 12, 2019 · 5c30ffd · 5c30ffd
1 parent 2dc7f91
commit 5c30ffd
Showing 1 changed file with 10 additions and 0 deletions.
diff --git a/svtools/lmerge.py b/svtools/lmerge.py
@@ -242,6 +242,16 @@ def create_merged_variant(BP, c, v_id, vcf, use_product, weighting_scheme='unwei
     [cipos95, ciend95]=getCI95( p_L, p_R, max_i_L, max_i_R)
     new_pos_L = new_start_L + max_i_L
     new_pos_R = new_start_R + max_i_R
+
+    # sometimes after looking at PRs, the left and right can be swapped.
+    # flip them back so downstream tools don't break.
+    if new_pos_R < new_pos_L:
+        new_pos_R, new_pos_L = new_pos_L, new_pos_R
+        cipos95, ciend95 = ciend95, cipos95
+        p_L, p_R = p_R, p_L
+        max_i_R, max_i_L = max_i_L, max_i_R
+
+
     BP0=BP[c[0]]
     A=BP0.l.rstrip().split('\t', 10)