Add test for bgzip, make sure peek is checked

pycompression · Jul 21, 2023 · 3ae0da4 · 3ae0da4
1 parent c7e8af4
commit 3ae0da4
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Showing 3 changed files with 11 additions and 1 deletion.
diff --git a/src/isal/igzip.py b/src/isal/igzip.py
@@ -266,7 +266,7 @@ def __init__(self, fp):
         self._new_member = True
         self._last_mtime = None
         self._read_buffer_size = READ_BUFFER_SIZE
-        if detect_bgzip(fp.peek(18)):
+        if hasattr(fp, "peek") and detect_bgzip(fp.peek(18)):
             # bgzip consists of puny little blocks of max 64K uncompressed data
             # so in practice probably more around 16K in compressed size. A
             # 128K buffer is a massive overshoot and slows down the

diff --git a/tests/data/test.fastq.bgzip.gz b/tests/data/test.fastq.bgzip.gz
diff --git a/tests/test_igzip.py b/tests/test_igzip.py
@@ -443,3 +443,13 @@ def test_concatenated_gzip():
     with igzip.open(concat, "rb") as igzip_h:
         result = igzip_h.read()
     assert data == result
+
+
+def test_bgzip():
+    bgzip_file = Path(__file__).parent / "data" / "test.fastq.bgzip.gz"
+    gzip_file = Path(__file__).parent / "data" / "test.fastq.gz"
+    with igzip.open(bgzip_file, "rb") as bgz:
+        bgz_data = bgz.read()
+    with igzip.open(gzip_file, "rb") as gz:
+        gz_data = gz.read()
+    assert bgz_data == gz_data