Use pipe when output file descriptor is not available

Author: Will-Tyler

vcztools/_vcztoolsmodule.c

@@ -480,10 +480,22 @@ static PyObject *
 VcfEncoder_encode_all(VcfEncoder *self, PyObject *args)
 {
 	bool allowed_threads = false;
+	int output_fd;
+	int is_pipe;
+	FILE* file = NULL;
 
     if (VcfEncoder_check_state(self) != 0) {
         goto out;
     }
+    if (!PyArg_ParseTuple(args, "ip", &output_fd, &is_pipe)) {
+    	goto out;
+    }
+
+    file = fdopen(output_fd, "w");
+
+    if (file == NULL) {
+    	goto out;
+    }
 
     Py_BEGIN_ALLOW_THREADS
 	allowed_threads = true;
@@ -512,14 +524,22 @@ VcfEncoder_encode_all(VcfEncoder *self, PyObject *args)
 					goto out;
 				}
 			} else {
-				puts(buf);
+				fputs(buf, file);
+				fputc('\n', file);
 				PyMem_RawFree(buf);
 				break;
 			} // if (line_length < 0)
 		} // while (true)
 	}
 
 out:
+	if (file != NULL) {
+		fflush(file);
+
+		if (is_pipe) {
+			fclose(file);
+		}
+	}
 	if (allowed_threads) {
     	Py_END_ALLOW_THREADS
     }

vcztools/vcf_writer.py

@@ -1,6 +1,7 @@
 import concurrent.futures
 import functools
 import io
+import os
 import re
 import sys
 from datetime import datetime
@@ -415,7 +416,21 @@ def c_chunk_to_vcf(
     if preceding_future:
         concurrent.futures.wait((preceding_future,))
 
-    encoder.encode_all()
+    output = output or sys.stdout
+    pipe = None
+    try:
+        output_fd = output.fileno()
+    except OSError:
+        pipe = os.pipe()
+        output_fd = pipe[1]
+
+    output.flush()
+    encoder.encode_all(output_fd, bool(pipe))
+
+    if pipe:
+        with io.FileIO(pipe[0], closefd=True) as pipe_reader:
+            output.write(pipe_reader.read().decode("ascii"))
+            output.flush()
 
 
 def _generate_header(ds, original_header, sample_ids, *, no_version: bool = False):