From 67ae775ae5059d0be12300bf60835803f0e4db8e Mon Sep 17 00:00:00 2001
From: donkirkby <donkirkby@gmail.com>
Date: Mon, 26 Apr 2021 14:55:11 -0700
Subject: [PATCH] Close #7 by accepting a few missing bases in a primer.

Also search for 250 bases from each end.
---
 gene_splicer/primer_finder.py       |  2 +-
 gene_splicer/primer_finder_class.py | 11 +++--------
 2 files changed, 4 insertions(+), 9 deletions(-)

diff --git a/gene_splicer/primer_finder.py b/gene_splicer/primer_finder.py
index 13fecdc..d4a5bbc 100644
--- a/gene_splicer/primer_finder.py
+++ b/gene_splicer/primer_finder.py
@@ -104,7 +104,7 @@ def find_primers(
         # The sequence type, can be either 'contigs' or 'conseqs'
         seqtype,
         sample_size=50,
-        extended_length=200,
+        extended_length=250,
         force_all_proviral=False):
     proviral_helper = ProviralHelper(force_all_proviral=force_all_proviral)
     errors = PrimerFinderErrors()
diff --git a/gene_splicer/primer_finder_class.py b/gene_splicer/primer_finder_class.py
index c119957..d5f8cd5 100644
--- a/gene_splicer/primer_finder_class.py
+++ b/gene_splicer/primer_finder_class.py
@@ -58,17 +58,13 @@ def find_longest_primer(self):
         else:
             hxb2_start_offset = 0
         hxb2_end_offset = 0
-        # Minus min_primer_length because the smallest primer we want to try looking for is min_primer_length nucleotides
+        # Minus min_primer_length because the smallest primer we want to try
+        # looking for is min_primer_length nucleotides
         for i in range(len(self.primer) - self.min_primer_length):
-            # print('i', i)
-            primer_substring = None
-
-            # If fwd
             if self.direction == 'fwd':
                 primer_substring = self.primer[i:]
                 hxb2_start_offset += 1
 
-            # If rev
             elif self.direction == 'rev':
                 if i == 0:
                     primer_substring = self.primer[:]
@@ -96,9 +92,8 @@ def validate(self):
             return
         elif len(self.sample_primer) >= 7:
             self.is_valid = True
-            if len(self.sample_primer) == self.primer_length:
+            if len(self.sample_primer) >= self.primer_length - 3:
                 self.is_full_length = True
-            # TODO: I should probably check that if the primer is not full length, that the start index is 0 for fwd and is len-1 for rev
             return
         else:
             sample_slice, hxb2_slice = self.get_slices()