strkit 0.24.1__tar.gz → 0.24.3__tar.gz

{strkit-0.24.1/strkit.egg-info → strkit-0.24.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: strkit
-Version: 0.24.1
+Version: 0.24.3
 Summary: A toolkit for analyzing variation in short(ish) tandem repeats.
 Home-page: https://github.com/davidlougheed/strkit
 Author: David Lougheed
@@ -27,7 +27,7 @@ Requires-Dist: pydantic<3,>=2.11.7
 Requires-Dist: scikit-learn<1.8,>=1.2.1
 Requires-Dist: scipy<1.17,>=1.10
 Requires-Dist: statsmodels<0.15,>=0.14.0
-Requires-Dist: strkit_rust_ext==0.24.1
+Requires-Dist: strkit_rust_ext==0.24.3
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{strkit-0.24.1 → strkit-0.24.3}/setup.py

@@ -23,7 +23,7 @@ setup(
         "scikit-learn>=1.2.1,<1.8",
         "scipy>=1.10,<1.17",
         "statsmodels>=0.14.0,<0.15",
-        "strkit_rust_ext==0.24.1",
+        "strkit_rust_ext==0.24.3",
     ],
 
     description="A toolkit for analyzing variation in short(ish) tandem repeats.",

strkit-0.24.3/strkit/VERSION

@@ -0,0 +1 @@
+0.24.3

{strkit-0.24.1 → strkit-0.24.3}/strkit/call/call_sample.py

@@ -447,7 +447,7 @@ def call_sample(
                         continue
                     rd += len(r["reads"])
                     nwr += 1
-                avg_read_depths_by_contig[results[0]["contig"]] = rd / nwr
+                avg_read_depths_by_contig[results[0]["contig"]] = (rd / nwr) if nwr else 0.0
                 total_read_depth += rd
                 total_loci_with_reads += nwr
             else:

{strkit-0.24.1 → strkit-0.24.3}/strkit/call/realign.py

@@ -63,7 +63,7 @@ def realign_read(
 
     lg.debug(f"Realigned {read_log_str}: scored {pr.score}; Flipped CIGAR: {pr.cigar.decode.decode('ascii')}")
 
-    res: STRkitAlignedCoords = get_aligned_pair_matches(decode_cigar_np(pr.cigar.seq), left_flank_coord, 0)
+    res: STRkitAlignedCoords = get_aligned_pair_matches(decode_cigar_np(pr.cigar.seq), left_flank_coord, 0, swap=True)
     return ret_q(res)
 
 

{strkit-0.24.1 → strkit-0.24.3/strkit.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: strkit
-Version: 0.24.1
+Version: 0.24.3
 Summary: A toolkit for analyzing variation in short(ish) tandem repeats.
 Home-page: https://github.com/davidlougheed/strkit
 Author: David Lougheed
@@ -27,7 +27,7 @@ Requires-Dist: pydantic<3,>=2.11.7
 Requires-Dist: scikit-learn<1.8,>=1.2.1
 Requires-Dist: scipy<1.17,>=1.10
 Requires-Dist: statsmodels<0.15,>=0.14.0
-Requires-Dist: strkit_rust_ext==0.24.1
+Requires-Dist: strkit_rust_ext==0.24.3
 Dynamic: author
 Dynamic: author-email
 Dynamic: classifier

{strkit-0.24.1 → strkit-0.24.3}/strkit.egg-info/requires.txt

@@ -7,4 +7,4 @@ pydantic<3,>=2.11.7
 scikit-learn<1.8,>=1.2.1
 scipy<1.17,>=1.10
 statsmodels<0.15,>=0.14.0
-strkit_rust_ext==0.24.1
+strkit_rust_ext==0.24.3

strkit-0.24.1/strkit/VERSION

@@ -1 +0,0 @@
-0.24.1