fix csq_load issue

jodyphelan · Jan 20, 2020 · e124e43 · e124e43
1 parent c1f7c5f
commit e124e43
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 3 deletions.
diff --git a/pathogenprofiler/vcf.py b/pathogenprofiler/vcf.py
@@ -80,6 +80,9 @@ def load_csq(self, ann_file = None):
                 continue
 
             for i in range(4,len(row)-4,5):
+                if row[i+1] == ".": continue
+                if row[i+1][0] == "@": continue
+
                 sample = row[i]
                 infos = [x.split("|") for x in row[i+1].split(",") if x!="."] + [x.split("|") for x in row[i+2].split(",") if x!="."]
                 info = None
@@ -92,8 +95,6 @@ def load_csq(self, ann_file = None):
                 ad = [int(x) if x!="." else 0 for x in row[i+4].split(",")]  if row[i+4]!="." else [0,100]
 
                 adr = {alleles[i]:d/sum(ad) for i,d in enumerate(ad)}
-                if row[i+1] == ".": continue
-                if row[i+1][0] == "@": continue
                 if info[-1] == "pseudogene": continue
                 gene_name = info[1]
                 gene_id = info[2] if info[2]!="" else gene_name

diff --git a/tbprofiler/__init__.py b/tbprofiler/__init__.py
@@ -4,4 +4,4 @@
 from .collate import *
 import os
 _ROOT = os.path.abspath(os.path.dirname(__file__))
-_VERSION = "2.8.3"
+_VERSION = "2.8.4"