svphaser 2.0.2__py3-none-any.whl → 2.0.6__py3-none-any.whl

svphaser/_version.py

@@ -28,7 +28,7 @@ version_tuple: VERSION_TUPLE
 commit_id: COMMIT_ID
 __commit_id__: COMMIT_ID
 
-__version__ = version = '2.0.2'
-__version_tuple__ = version_tuple = (2, 0, 2)
+__version__ = version = '2.0.6'
+__version_tuple__ = version_tuple = (2, 0, 6)
 
 __commit_id__ = commit_id = None

svphaser/phasing/algorithms.py

@@ -46,26 +46,27 @@ def classify_haplotype(
     *,
     min_support: int = 10,
     major_delta: float = 0.70,
-    equal_delta: float = 0.25,
+    equal_delta: float = 0.10,
 ) -> tuple[str, int]:
-    """Return (GT, GQ) using ratio thresholds and an overflow-safe GQ."""
     total = n1 + n2
-
     if n1 < min_support and n2 < min_support:
         return "./.", 0
     if total == 0:
         return "./.", 0
 
     gq = phasing_gq(n1, n2)
+
+    # 1) near-tie FIRST → homozygous phased
+    if abs(n1 - n2) / total <= equal_delta:
+        return "1|1", gq  # includes exactly 50/50
+
+    # 2) strong majority → heterozygous phased
     r1 = n1 / total
     r2 = n2 / total
-
     if r1 >= major_delta:
-        gt = "1|0"
-    elif r2 >= major_delta:
-        gt = "0|1"
-    elif abs(n1 - n2) / total <= equal_delta:
-        gt = "1|1"
-    else:
-        gt = "./."
-    return gt, gq
+        return "1|0", gq
+    if r2 >= major_delta:
+        return "0|1", gq
+
+    # 3) otherwise ambiguous
+    return "./.", gq

{svphaser-2.0.2.dist-info → svphaser-2.0.6.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: svphaser
-Version: 2.0.2
+Version: 2.0.6
 Summary: Structural-variant phasing from HP-tagged long-read BAMs
 Project-URL: Homepage, https://github.com/your-org/svphaser
 Project-URL: Issues, https://github.com/your-org/svphaser/issues

{svphaser-2.0.2.dist-info → svphaser-2.0.6.dist-info}/RECORD

@@ -1,16 +1,16 @@
 svphaser/__init__.py,sha256=ytsjARd0ZTn3FbN2BEvpPXygBwQyLiQZ5VB2SyXKL18,2485
 svphaser/__main__.py,sha256=lWe9boXc4JIpJEknv9dXqSsjS1Glk_FnYV9eBzUEzA0,86
-svphaser/_version.py,sha256=UFd-y4dR-HVHWzUJlgmJ3T05hh9C4Q-la-D9QTIoZw0,704
+svphaser/_version.py,sha256=bTAFMFvMAxBeOekZBtqvKDMVXKX-jvNDCL0lbfqDCt0,704
 svphaser/cli.py,sha256=Qbo0IPsm6_Uhj2Ri_fuqX4NJlxC9APl70rtM0vOU4jk,5335
 svphaser/logging.py,sha256=yw7Z8az-sZL-x4qhvPmu7aGVLbhSOYiSdrNqCO8bVtw,841
 svphaser/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 svphaser/phasing/__init__.py,sha256=RcXg2EGc7Dyuq8wDP-bJmtVNKs8f3YqByjTel0mMujM,464
 svphaser/phasing/_workers.py,sha256=C7YKx9YYq8stoyMeVQsmEnMgTqulALCjWHhhAWb1MQ8,2862
-svphaser/phasing/algorithms.py,sha256=9UetPSi5BDCvvhmCn8t1ia08lupqTOI-68azwK46hek,1745
+svphaser/phasing/algorithms.py,sha256=EEc2_ix7v8Z4d_dO2yOdgPvxTAM6ekWo0X0bDyvFjyI,1810
 svphaser/phasing/io.py,sha256=RXsCJb88zPB1tAHhlQ2tT3kHo-inD-tsQTCyWNUzM7o,9029
 svphaser/phasing/types.py,sha256=b0K9ORyuwv3O1VbCm_ml1nLpQQv_dJsMKO8p4uTRn4k,814
-svphaser-2.0.2.dist-info/METADATA,sha256=7kPl92IMR91GItQ_24ZDgGr8ITh8j5UAeqvZKz3TdRE,6430
-svphaser-2.0.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-svphaser-2.0.2.dist-info/entry_points.txt,sha256=YFeRJLvcvTc4dazgyVOg3HJ4fNrvBrVDaPX6ULapqeU,46
-svphaser-2.0.2.dist-info/licenses/LICENSE,sha256=qsY5iOcewwIwvhQbj7naSP6tpJAc05Mv0DfhrouPoBU,1102
-svphaser-2.0.2.dist-info/RECORD,,
+svphaser-2.0.6.dist-info/METADATA,sha256=cT_9pJI-1dRJwVWt_ULrr8TlNZPpr7AJK6BB0A8EOyo,6430
+svphaser-2.0.6.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+svphaser-2.0.6.dist-info/entry_points.txt,sha256=YFeRJLvcvTc4dazgyVOg3HJ4fNrvBrVDaPX6ULapqeU,46
+svphaser-2.0.6.dist-info/licenses/LICENSE,sha256=qsY5iOcewwIwvhQbj7naSP6tpJAc05Mv0DfhrouPoBU,1102
+svphaser-2.0.6.dist-info/RECORD,,