Add HTSFile.flush() for flushing output streams

Enables programs to explicitly flush AlignmentFile and
VariantFile objects. Fixes #1299.

pysam/libchtslib.pxd

@@ -573,6 +573,12 @@ cdef extern from "htslib/hts.h" nogil:
     # @param mode     Open mode, as per hts_open()
     htsFile *hts_hopen(hFILE *fp, const char *fn, const char *mode)
 
+    # @abstract  For output streams, flush any buffered data
+    # @param fp  The file handle to be flushed
+    # @return    0 for success, or negative if an error occurred.
+    # @since     1.14
+    int hts_flush(htsFile *fp)
+
     # @abstract  Close a file handle, flushing buffered data for output streams
     # @param fp  The file handle to be closed
     # @return    0 for success, or negative if an error occurred.

pysam/libchtslib.pyi

@@ -64,6 +64,7 @@ class HTSFile:
     @property
     def duplicate_filehandle(self) -> bool: ...
     def close(self) -> None: ...
+    def flush(self) -> None: ...
     def check_truncation(self, ignore_truncation: bool = ...) -> None: ...
     @property
     def category(self) -> str: ...

pysam/libchtslib.pyx

@@ -338,6 +338,12 @@ cdef class HTSFile(object):
             hts_close(self.htsfile)
             self.htsfile = NULL
 
+    def flush(self):
+        """Flush any buffered data to the underlying output stream."""
+        if self.htsfile:
+            if hts_flush(self.htsfile) < 0:
+                raise OSError(errno, f'Flushing {type(self).__name__} failed', force_str(self.filename))
+
     def check_truncation(self, ignore_truncation=False):
         """Check if file is truncated."""
         if not self.htsfile: