Merge branch 'master' of https://github.com/hall-lab/svtools into dev…

…elop
hall-lab · Sep 4, 2019 · 9287ed9 · 9287ed9
2 parents 6c5e80e + 5b3289b
commit 9287ed9
Showing 1 changed file with 10 additions and 0 deletions.
diff --git a/svtools/lmerge.py b/svtools/lmerge.py
@@ -243,6 +243,16 @@ def create_merged_variant(BP, c, v_id, vcf, use_product, weighting_scheme='unwei
     new_pos_L = new_start_L + max_i_L
     new_pos_R = new_start_R + max_i_R
     BP0=BP[c[0]]
+
+    # 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 and BP0.sv_type != 'BND':
+        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
+
+
     A=BP0.l.rstrip().split('\t', 10)
 
     ALT = ''