From bd7b64068cfbbb80943a30ca84b368ede02bd315 Mon Sep 17 00:00:00 2001
From: Dillon Barker <dor.barker@gmail.com>
Date: Mon, 29 Oct 2018 16:34:01 -0600
Subject: [PATCH] fix bug with short matches

---
 src/allele_call.py | 1 +
 src/update.py      | 4 +++-
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/allele_call.py b/src/allele_call.py
index f37a8bf..739d929 100644
--- a/src/allele_call.py
+++ b/src/allele_call.py
@@ -158,6 +158,7 @@ def unpack_value(value):
             'QueryName':            blast_hit['qseqid'],
             'SubjName':             blast_hit['sseqid'],
             'PercentIdentity':      blast_hit['pident'],
+            'PercentLength':        blast_hit['length'] / blast_hit['qlen'],
             'SubjectStartIndex':    blast_hit['sstart'],
             'SubjectEndIndex':      blast_hit['send'],
             'QueryStartIndex':      blast_hit['qstart'],
diff --git a/src/update.py b/src/update.py
index 624ce33..9703b1d 100644
--- a/src/update.py
+++ b/src/update.py
@@ -23,7 +23,9 @@ def update_locus(gene: Dict[str, Union[str, int, bool, float]],
     if not gene['BlastResult']:
         return None, None
 
-    if gene['CorrectMarkerMatch'] or gene['IsContigTruncation']:
+    if any((gene['CorrectMarkerMatch'],
+            gene['IsContigTruncation'],
+            gene['PercentLength'] < 1)):
 
         return None, None