small bugfix in _covers_index

hyraxbio · Mar 9, 2017 · a2925fb · a2925fb
1 parent f7ec3ce
commit a2925fb
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diff --git a/seq2simulate/diversity.py b/seq2simulate/diversity.py
@@ -375,6 +375,7 @@ def _simulate_inversions(sequences, freq=0.3, max_length=200, min_length=15):
                 ins_start = random.randrange(0, len(seq)-min_length)
                 ins_length = random.randint(min_length, min(max_length, len(seq)-ins_start))
                 inverted_sequence = seq[ins_start:ins_start + ins_length][::-1]
+                uninverted_seq = seq[ins_start:ins_start + ins_length]
                 new_sequence = seq[0:ins_start] + inverted_sequence + seq[ins_start + ins_length:]
                 if _get_n_stop_codons(new_sequence) <= _get_n_stop_codons(seq):
                     new_stops_introduced = False

diff --git a/seq2simulate/run_make_proviral_data.py b/seq2simulate/run_make_proviral_data.py
@@ -361,7 +361,7 @@ def _is_inversion(sam_line, seq_diffs):
     return False
 
 def _covers_index(read_start, read_end, index):
-    return True if read_start <= index <= read_end else False
+    return True if read_start <= index < read_end else False
 
 def sample_fastq(n_reads, fastq1=None, fastq2=None):