pav3 3.0.0.dev20__tar.gz → 3.0.0.dev21__tar.gz

{pav3-3.0.0.dev20/src/pav3.egg-info → pav3-3.0.0.dev21}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pav3
-Version: 3.0.0.dev20
+Version: 3.0.0.dev21
 Summary: Assembly-based variant discovery
 License-Expression: MIT
 Requires-Python: >=3.12

{pav3-3.0.0.dev20 → pav3-3.0.0.dev21}/src/pav3/__init__.py

@@ -1,6 +1,6 @@
 """PAV Python library routines."""
 
-__version__ = '3.0.0.dev20'
+__version__ = '3.0.0.dev21'
 
 __all__ = [
     'align',

{pav3-3.0.0.dev20 → pav3-3.0.0.dev21}/src/pav3/align/features.py

@@ -335,13 +335,16 @@ class FeatureGenerator:
         return df.with_columns(
             df
             .select(
-                pl.col('score') / (
-                    (
-                        pl.col('qry_end') - pl.col('qry_pos')
+                (
+                    pl.col('score')
+                    / (
+                        (
+                            pl.col('qry_end') - pl.col('qry_pos')
+                        )
+                        .fill_null(0.0)
+                        .map_elements(self.score_model.match, return_dtype=pl.Float64)
                     )
-                    .fill_null(0.0)
-                    .map_elements(self.score_model.match, return_dtype=pl.Float32)
-                )
+                ).cast(pl.Float32)
             )
             .to_series()
             .alias('score_prop')
@@ -377,15 +380,18 @@ class FeatureGenerator:
             )
             .with_columns(
                 (
-                    pl.col('score_mm') / (
-                        (
-                            pl.col("_op_len") * (
-                                pl.col("_op_code").list.eval(pl.element().is_in([op.EQ, op.X]))
+                    (
+                        pl.col('score_mm')
+                        / (
+                            (
+                                pl.col("_op_len") * (
+                                    pl.col("_op_code").list.eval(pl.element().is_in([op.EQ, op.X]))
+                                )
                             )
+                            .list.sum()
+                            .map_elements(self.score_model.match, return_dtype=pl.Float64)
                         )
-                        .list.sum()
-                        .map_elements(self.score_model.match, return_dtype=pl.Float32)
-                    )
+                    ).cast(pl.Float32)
                 )
                 .alias('score_mm_prop')
             )

{pav3-3.0.0.dev20 → pav3-3.0.0.dev21}/src/pav3/align/lift.py

@@ -532,7 +532,7 @@ class AlignLift:
         """
         lift_pairs = get_lift_pairs(
             a=self.to_ref(region.chrom, region.pos),
-            b=self.to_ref(region.chrom, region.end),
+            b=self.to_ref(region.chrom, region.end - 1),
             same_align=same_align,
             single_align=single_align,
             multi=multi,
@@ -550,7 +550,7 @@ class AlignLift:
         return Region(
             chrom=pos['lift_id'],
             pos=pos['lift_pos'],
-            end=end['lift_pos'],
+            end=end['lift_pos'] + 1,
             is_rev=pos['is_rev'],
             pos_align_index=pos['align_index'],
             end_align_index=end['align_index'],
@@ -578,7 +578,7 @@ class AlignLift:
         """
         lift_pairs = get_lift_pairs(
             a=self.to_qry(region.chrom, region.pos),
-            b=self.to_qry(region.chrom, region.end),
+            b=self.to_qry(region.chrom, region.end - 1),
             same_align=same_align,
             single_align=single_align,
             multi=multi,
@@ -596,7 +596,7 @@ class AlignLift:
         return Region(
             chrom=pos['lift_id'],
             pos=pos['lift_pos'],
-            end=end['lift_pos'],
+            end=end['lift_pos'] + 1,
             is_rev=pos['is_rev'],
             pos_align_index=pos['align_index'],
             end_align_index=end['align_index'],

{pav3-3.0.0.dev20 → pav3-3.0.0.dev21}/src/pav3/align/score.py

@@ -163,7 +163,8 @@ class ScoreModel(ABC):
             .select(pl.col('align_ops'))
             .to_series()
             .map_elements(op.row_to_arr, return_dtype=pl.Object)
-            .map_elements(lambda op_arr: np.float32(self.score_op_arr(op_arr)), return_dtype=pl.Float32)
+            .map_elements(lambda op_arr: self.score_op_arr(op_arr), return_dtype=pl.Float64)
+            .cast(pl.Float32)
         )
 
         # A pure polars implementation is slower:

{pav3-3.0.0.dev20 → pav3-3.0.0.dev21}/src/pav3/data/workflow/rules/align.smk

@@ -126,7 +126,7 @@ rule align_tables:
             df_qry_fai=df_qry_fai,
             score_model=score_model,
             lc_model=lc_model,
-            ref_fa_filename=ref_fa_filename
+            ref_fa_filename=ref_fa_filename,
         )
 
         if pav_params.debug:

{pav3-3.0.0.dev20 → pav3-3.0.0.dev21}/src/pav3/dev/sm.py

@@ -9,7 +9,10 @@ __all__ = [
 import re
 from typing import Optional, Iterable
 
-from snakemake.io import Namedlist
+try:
+    from snakemake.io import Namedlist
+except ImportError:
+    from snakemake.iocontainers import Namedlist
 
 
 def strip_and_format(

{pav3-3.0.0.dev20 → pav3-3.0.0.dev21/src/pav3.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: pav3
-Version: 3.0.0.dev20
+Version: 3.0.0.dev21
 Summary: Assembly-based variant discovery
 License-Expression: MIT
 Requires-Python: >=3.12