From 4d1b5d84271104a16e1f9cb312c5e167f8dc638c Mon Sep 17 00:00:00 2001
From: Danilo Horta <danilo.horta@pm.me>
Date: Mon, 27 Nov 2023 16:25:54 +0000
Subject: [PATCH] Update c-core to v0.13.12 and add cut_ga parameter

---
 python-core/build_ext.py              | 2 +-
 python-core/deciphon_core/interface.h | 3 ++-
 python-core/deciphon_core/params.py   | 8 ++++++--
 python-core/pyproject.toml            | 2 +-
 python-core/tests/test_scan.py        | 2 +-
 5 files changed, 11 insertions(+), 6 deletions(-)

diff --git a/python-core/build_ext.py b/python-core/build_ext.py
index 15e64bb..8e68ebe 100644
--- a/python-core/build_ext.py
+++ b/python-core/build_ext.py
@@ -68,7 +68,7 @@ class Ext:
     Ext(
         "EBI-Metagenomics",
         "deciphon",
-        "c-core-v0.13.11",
+        "c-core-v0.13.12",
         "./c-core",
         CMAKE_OPTS + CPM_OPTS,
     ),
diff --git a/python-core/deciphon_core/interface.h b/python-core/deciphon_core/interface.h
index 1777b20..6748756 100644
--- a/python-core/deciphon_core/interface.h
+++ b/python-core/deciphon_core/interface.h
@@ -8,8 +8,9 @@ struct params
   int  num_threads;
   bool multi_hits;
   bool hmmer3_compat;
+  bool cut_ga;
 };
-int params_setup(struct params *, int num_threads, bool multi_hits, bool hmmer3_compat);
+int params_setup(struct params *, int num_threads, bool multi_hits, bool hmmer3_compat, bool cut_ga);
 
 // Press
 struct press *press_new(void);
diff --git a/python-core/deciphon_core/params.py b/python-core/deciphon_core/params.py
index 904a536..ccaaf0d 100644
--- a/python-core/deciphon_core/params.py
+++ b/python-core/deciphon_core/params.py
@@ -5,12 +5,16 @@
 
 
 class Params:
-    def __init__(self, num_threads: int, multi_hits: bool, hmmer3_compat: bool):
+    def __init__(
+        self, num_threads: int, multi_hits: bool, hmmer3_compat: bool, cut_ga: bool
+    ):
         self._cptr = ffi.new("struct params *")
         if self._cptr == ffi.NULL:
             raise MemoryError()
 
-        if rc := lib.params_setup(self._cptr, num_threads, multi_hits, hmmer3_compat):
+        if rc := lib.params_setup(
+            self._cptr, num_threads, multi_hits, hmmer3_compat, cut_ga
+        ):
             raise DeciphonError(rc)
 
     @property
diff --git a/python-core/pyproject.toml b/python-core/pyproject.toml
index 9b71828..47327ac 100644
--- a/python-core/pyproject.toml
+++ b/python-core/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "deciphon-core"
-version = "0.18.12"
+version = "0.18.13"
 description = "Python wrapper around the Deciphon C library"
 authors = ["Danilo Horta <horta@ebi.ac.uk>"]
 license = "MIT"
diff --git a/python-core/tests/test_scan.py b/python-core/tests/test_scan.py
index 611616e..518e255 100644
--- a/python-core/tests/test_scan.py
+++ b/python-core/tests/test_scan.py
@@ -34,7 +34,7 @@ def test_scan(tmp_path, files_path: Path):
 
     hmmfile = H3File(hmm)
     hmmfile.ensure_pressed()
-    params = Params(num_threads=1, multi_hits=True, hmmer3_compat=False)
+    params = Params(num_threads=1, multi_hits=True, hmmer3_compat=False, cut_ga=True)
     snapfile = NewSnapFile(path=Path("snap.dcs").absolute())
 
     with SchedContext(hmmfile) as sched: