Add tsk_treeseq_decode_alignments (#3324)

* Fix build warning

* Add tsk_treeseq_decode_alignments

Author: benjeffery

c/CHANGELOG.rst

@@ -2,10 +2,24 @@
 Unreleased
 ----------
 
+**Breaking changes**
+
+- ``trees.c`` now depends on ``genotypes.c`` (via ``tskit/genotypes.h``) and must
+  be built and linked together with it.
+  (:user:`benjeffery`, :pr:`3324`)
+
+
+**Features**
+
 - ``tsk_variant_init`` and associated variant decoding methods now
   fully support TSK_ISOLATED_NOT_MISSING not being set for internal nodes.
   (:user:`benjeffery`, :pr:`3313`)
 
+- Add ``tsk_treeseq_decode_alignments`` to decode full-length reference-based
+  sequence alignments for specified nodes over a genomic interval, respecting
+  ``TSK_ISOLATED_NOT_MISSING`` semantics.
+  (:user:`benjeffery` , :pr:`3324`, :issue:`3319`)
+
 
 --------------------
 [1.2.0] - 2025-09-24

c/tests/test_file_format.c

@@ -872,7 +872,8 @@ test_load_bad_file_formats(void)
         ret = tsk_table_collection_dump(&tables, _tmp_file_name, 0);
         CU_ASSERT_EQUAL_FATAL(ret, 0);
 
-        truncate(_tmp_file_name, offset);
+        ret2 = truncate(_tmp_file_name, offset);
+        CU_ASSERT_EQUAL_FATAL(ret2, 0);
         ret = tsk_table_collection_load(&tables, _tmp_file_name, TSK_NO_INIT);
         CU_ASSERT_EQUAL_FATAL(ret ^ (1 << TSK_KAS_ERR_BIT), KAS_ERR_BAD_FILE_FORMAT);
         tsk_table_collection_free(&tables);