strkit 0.8.0a6__tar.gz → 0.8.0a7__tar.gz

{strkit-0.8.0a6/strkit.egg-info → strkit-0.8.0a7}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: strkit
-Version: 0.8.0a6
+Version: 0.8.0a7
 Summary: A toolkit for analyzing variation in short(ish) tandem repeats.
 Home-page: https://github.com/davidlougheed/strkit
 Author: David Lougheed

strkit-0.8.0a7/strkit/VERSION

@@ -0,0 +1 @@
+0.8.0a7

{strkit-0.8.0a6 → strkit-0.8.0a7}/strkit/call/caller/call_locus.py

@@ -712,7 +712,7 @@ def call_locus(
 
         for rn, read in read_dict_items:
             snvs = get_read_snvs(
-                read["_qs"], read_pairs[rn], ref_cache, left_most_coord, right_most_coord, left_coord_adj,
+                read["_qs"], read_pairs[rn], ref_cache, left_most_coord, left_coord_adj,
                 right_coord_adj)
             locus_snvs.update(snvs.keys())
             read_dict[rn]["snv"] = snvs

{strkit-0.8.0a6 → strkit-0.8.0a7}/strkit/call/caller/snvs.py

@@ -25,7 +25,6 @@ def _get_read_snvs_meticulous(
     pairs: list[tuple[int, int], ...],
     ref_seq: str,
     ref_coord_start: int,
-    ref_coord_end: int,
     tr_start_pos: int,
     tr_end_pos: int,
     contiguous_threshold: int = 5,
@@ -39,11 +38,6 @@ def _get_read_snvs_meticulous(
 
     snvs: dict[int, str] = {}
 
-    fm_qp, fm_rp = pairs[0]
-    lm_qp, lm_rp = pairs[-1]
-
-    read_ref_sequence: str = ref_seq[fm_rp-ref_coord_start:lm_rp-ref_coord_end+1]
-
     lhs_contiguous: int = 0
     rhs_contiguous: int = 0
     last_rp: int = -1
@@ -55,7 +49,7 @@ def _get_read_snvs_meticulous(
             continue
 
         read_base = query_sequence[read_pos]
-        ref_base = read_ref_sequence[ref_pos - fm_rp]
+        ref_base = ref_seq[ref_pos - ref_coord_start]
 
         if read_base == ref_base and (ref_pos - last_rp == 1 or last_rp == -1):
             if snv_group:
@@ -92,7 +86,6 @@ def get_read_snvs(
     pairs: list[tuple[int, int], ...],
     ref_seq: str,
     ref_coord_start: int,
-    ref_coord_end: int,
     tr_start_pos: int,
     tr_end_pos: int,
     contiguous_threshold: int = 5,
@@ -107,15 +100,10 @@ def get_read_snvs(
 
     snvs: dict[int, str] = {}
 
-    fm_qp, fm_rp = pairs[0]
-    lm_qp, lm_rp = pairs[-1]
-
-    read_ref_sequence: str = ref_seq[fm_rp-ref_coord_start:lm_rp-ref_coord_end]
-
     for read_pos, ref_pos in pairs:
         if tr_start_pos <= ref_pos < tr_end_pos:  # base is in the tandem repeat itself; skip it
             continue
-        if (read_base := query_sequence[read_pos]) != read_ref_sequence[ref_pos - fm_rp]:
+        if (read_base := query_sequence[read_pos]) != ref_seq[ref_pos - ref_coord_start]:
             snvs[ref_pos] = read_base
 
     if len(snvs) >= too_many_snvs_threshold:  # TOO MANY, some kind of mismapping going on
@@ -124,7 +112,6 @@ def get_read_snvs(
             pairs,
             ref_seq,
             ref_coord_start,
-            ref_coord_end,
             tr_start_pos,
             tr_end_pos,
             contiguous_threshold,

{strkit-0.8.0a6 → strkit-0.8.0a7/strkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: strkit
-Version: 0.8.0a6
+Version: 0.8.0a7
 Summary: A toolkit for analyzing variation in short(ish) tandem repeats.
 Home-page: https://github.com/davidlougheed/strkit
 Author: David Lougheed

strkit-0.8.0a6/strkit/VERSION

@@ -1 +0,0 @@
-0.8.0a6