update C code to version 0.99.12 (#122)

Remove use of TSK_NO_BUILD_INDEXES

Author: molpopgen

src/table_collection.rs

@@ -447,16 +447,13 @@ impl TableCollection {
 
     /// Dump the table collection to file.
     ///
-    /// # Note
-    ///
-    /// This function by default uses the flag TSK_NO_BUILD_INDEXES.
     pub fn dump(&self, filename: &str, options: TableOutputOptions) -> TskReturnValue {
         let c_str = std::ffi::CString::new(filename).unwrap();
         let rv = unsafe {
             ll_bindings::tsk_table_collection_dump(
                 self.as_ptr() as *mut ll_bindings::tsk_table_collection_t,
                 c_str.as_ptr(),
-                options.bits() | ll_bindings::TSK_NO_BUILD_INDEXES,
+                options.bits(),
             )
         };
 

src/trees.rs

@@ -915,16 +915,13 @@ impl TreeSequence {
     ///   This behavior may change in a future release, which could
     ///   break `API`.
     ///
-    /// # Note
-    ///
-    /// This function always sets the flag TSK_NO_BUILD_INDEXES.
     pub fn dump(&self, filename: &str, options: TableOutputOptions) -> TskReturnValue {
         let c_str = std::ffi::CString::new(filename).unwrap();
         let rv = unsafe {
             ll_bindings::tsk_treeseq_dump(
                 self.as_ptr() as *mut ll_bindings::tsk_treeseq_t,
                 c_str.as_ptr(),
-                options.bits() | ll_bindings::TSK_NO_BUILD_INDEXES,
+                options.bits(),
             )
         };
 

subprojects/tskit/tskit/core.c

@@ -357,6 +357,9 @@ tsk_strerror_internal(int err)
         case TSK_ERR_NONBINARY_MUTATIONS_UNSUPPORTED:
             ret = "Only binary mutations are supported for this operation";
             break;
+        case TSK_ERR_CANNOT_EXTEND_FROM_SELF:
+            ret = "Tables can only be extended using rows from a different table";
+            break;
 
         /* Stats errors */
         case TSK_ERR_BAD_NUM_WINDOWS:

subprojects/tskit/tskit/core.h

@@ -129,7 +129,7 @@ to the API or ABI are introduced, i.e., the addition of a new function.
 The library patch version. Incremented when any changes not relevant to the
 to the API or ABI are introduced, i.e., internal refactors of bugfixes.
 */
-#define TSK_VERSION_PATCH   11
+#define TSK_VERSION_PATCH   12
 /** @} */
 
 /* Node flags */
@@ -274,6 +274,7 @@ not found in the file.
 #define TSK_ERR_SORT_OFFSET_NOT_SUPPORTED                           -803
 #define TSK_ERR_NONBINARY_MUTATIONS_UNSUPPORTED                     -804
 #define TSK_ERR_MIGRATIONS_NOT_SUPPORTED                            -805
+#define TSK_ERR_CANNOT_EXTEND_FROM_SELF                             -806
 
 /* Stats errors */
 #define TSK_ERR_BAD_NUM_WINDOWS                                     -900