svphaser 2.0.1__py3-none-any.whl → 2.0.2__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 = '2.0.1'
-__version_tuple__ = version_tuple = (2, 0, 1)
+__version__ = version = '2.0.2'
+__version_tuple__ = version_tuple = (2, 0, 2)
 
 __commit_id__ = commit_id = None

svphaser/phasing/io.py

@@ -157,7 +157,7 @@ def _vcf_info_lookup(
                 info_dict[info_key] = v
         lookup[key] = {
             "REF": rec.REF,
-            "ALT": rec.ALT[0] if rec.ALT else "<N>",
+            "ALT": ",".join(rec.ALT) if rec.ALT else "<N>",
             "QUAL": rec.QUAL if rec.QUAL is not None else ".",
             "FILTER": rec.FILTER if rec.FILTER else "PASS",
             "INFO": info_dict,
@@ -196,17 +196,18 @@ def _write_headers(
     out.write("#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\t" + sample_name + "\n")
 
 
-def _compose_info_str(
-    orig_info: dict[str, object],
-    svtype: object,
-    gq_label: object,
-) -> str:
+def _compose_info_str(orig_info: dict[str, object], svtype: object, gq_label: object) -> str:
     """Compose the INFO string with SVTYPE first, original keys (no duplicate), then GQBIN."""
     items: list[str] = []
     for k, v in orig_info.items():
         if k == "SVTYPE":
             continue
         items.append(f"{k}={v}")
+        # treat boolean True as a FLAG (bare key). Keep everything else as k=v.
+        if v is True:
+            items.append(k)
+        else:
+            items.append(f"{k}={v}")
     if svtype:
         items.insert(0, f"SVTYPE={svtype}")
     if gq_label is not None and pd.notnull(gq_label):

{svphaser-2.0.1.dist-info → svphaser-2.0.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: svphaser
-Version: 2.0.1
+Version: 2.0.2
 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-2.0.1.dist-info → svphaser-2.0.2.dist-info}/RECORD

@@ -1,16 +1,16 @@
 svphaser/__init__.py,sha256=ytsjARd0ZTn3FbN2BEvpPXygBwQyLiQZ5VB2SyXKL18,2485
 svphaser/__main__.py,sha256=lWe9boXc4JIpJEknv9dXqSsjS1Glk_FnYV9eBzUEzA0,86
-svphaser/_version.py,sha256=b81iV_6_GhhfUN6bognTzQ8RMeyOUj9vn-DmcuKf2qU,704
+svphaser/_version.py,sha256=UFd-y4dR-HVHWzUJlgmJ3T05hh9C4Q-la-D9QTIoZw0,704
 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/io.py,sha256=iftFNePolH9QMa_Pr9ZO0Ts1zbelHc1FgdL-AuuMLFo,8856
+svphaser/phasing/io.py,sha256=RXsCJb88zPB1tAHhlQ2tT3kHo-inD-tsQTCyWNUzM7o,9029
 svphaser/phasing/types.py,sha256=b0K9ORyuwv3O1VbCm_ml1nLpQQv_dJsMKO8p4uTRn4k,814
-svphaser-2.0.1.dist-info/METADATA,sha256=msfqHpg-xiDVaqgP6li7e8iua50aLPZ7i0D28RCMFaQ,6430
-svphaser-2.0.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-svphaser-2.0.1.dist-info/entry_points.txt,sha256=YFeRJLvcvTc4dazgyVOg3HJ4fNrvBrVDaPX6ULapqeU,46
-svphaser-2.0.1.dist-info/licenses/LICENSE,sha256=qsY5iOcewwIwvhQbj7naSP6tpJAc05Mv0DfhrouPoBU,1102
-svphaser-2.0.1.dist-info/RECORD,,
+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,,