Expose some bwa indel parameters through the off-target checker.

prymer/offtarget/bwa.py

@@ -232,6 +232,7 @@ def __init__(
         max_mismatches_in_seed: int = 3,
         max_gap_opens: int = 0,
         max_gap_extensions: int = -1,
+        min_indel_to_end_distance: int = 3,
         seed_length: int = 20,
         reverse_complement: bool = False,
         include_alt_hits: bool = False,
@@ -248,6 +249,8 @@ def __init__(
             max_gap_opens: the maximum number of gap opens allowed in the full query sequence
             max_gap_extensions: the maximum number of gap extensions allowed in the full query
                                 sequence
+            min_indel_to_end_distance: do not place an indel within this many bp of the ends of
+                the query sequence
             seed_length: the length of the seed region
             reverse_complement: reverse complement each query sequence before alignment
             include_alt_hits: if true include hits to references with names ending in _alt,
@@ -288,6 +291,8 @@ def __init__(
             f"{max_gap_opens}",
             "-e",
             f"{max_gap_extensions}",
+            "-i",
+            f"{min_indel_to_end_distance}",
             "-l",
             f"{seed_length}",
             "-k",

prymer/offtarget/offtarget_detector.py

@@ -159,7 +159,9 @@ def __init__(
         three_prime_region_length: int,
         max_mismatches_in_three_prime_region: int,
         max_mismatches: int,
-        max_amplicon_size: int,
+        max_gap_opens: int = 0,
+        max_gap_extends: int = -1,
+        max_amplicon_size: int = 1000,
         min_primer_pair_hits: int = 1,
         cache_results: bool = True,
         threads: Optional[int] = None,
@@ -201,6 +203,12 @@ def __init__(
                 three_prime_region_length
             max_mismatches: the maximum number of mismatches allowed in the full length primer
                 (including any in the three prime region)
+            max_gap_opens: the maximum number of gaps (insertions or deletions) allowable in an
+                alignment of a oligo to the reference
+            max_gap_extends: the maximum number of gap extensions allowed; extending a gap
+                beyond a single base costs 1 gap extension.  Can be set to -1 to allow
+                unlimited extensions up to max diffs (aka max mismatches), while disallowing
+                "long gaps".
             max_amplicon_size: the maximum amplicon size to consider amplifiable
             cache_results: if True, cache results for faster re-querying
             threads: the number of threads to use when invoking bwa
@@ -220,6 +228,8 @@ def __init__(
             seed_length=three_prime_region_length,
             max_mismatches_in_seed=max_mismatches_in_three_prime_region,
             max_mismatches=max_mismatches,
+            max_gap_opens=max_gap_opens,
+            max_gap_extensions=max_gap_extends,
             max_hits=max_primer_hits,
         )
         self._max_primer_hits = max_primer_hits