Fix broken --reorder for paired minimap2 under Linux

bede · Jan 13, 2024 · 422ce2e · 422ce2e
1 parent ae632d7
commit 422ce2e
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Showing 2 changed files with 22 additions and 5 deletions.
diff --git a/src/hostile/aligner.py b/src/hostile/aligner.py
@@ -166,8 +166,10 @@ def gen_paired_clean_cmd(
             " | samtools view -hF 12 -" if invert else " | samtools view -f 12 -"
         )
         reorder_cmd = ""
-        if reorder:  # Under MacOS, Bowtie2's native --reorder is very slow
-            if util.get_platform() == "darwin":
+        if self.name == "Bowtie2" and reorder:
+            if (
+                util.get_platform() == "darwin"
+            ):  # Under MacOS, Bowtie2's native --reorder is very slow
                 reorder_cmd = " | samtools sort -n -O sam -@ 6 -m 1G" if reorder else ""
             else:  # Under Linux, Bowtie2's --reorder option works very well
                 reorder_cmd = ""

diff --git a/tests/test_all.py b/tests/test_all.py
@@ -558,7 +558,6 @@ def test_invert_single():
         fastqs=[data_dir / "sars-cov-2_1_1.fastq"],
         aligner=lib.ALIGNER.minimap2,
         index=data_dir / "sars-cov-2/sars-cov-2.fasta.gz",
-        reorder=True,
         out_dir=out_dir,
         invert=True,
         force=True,
@@ -568,6 +567,24 @@ def test_invert_single():
 
 
 def test_invert_paired():
+    stats = lib.clean_paired_fastqs(
+        fastqs=[
+            (
+                data_dir / "sars-cov-2_1_1.fastq",
+                data_dir / "sars-cov-2_1_2.fastq",
+            ),
+        ],
+        aligner=lib.ALIGNER.bowtie2,
+        index=data_dir / "sars-cov-2/sars-cov-2",
+        out_dir=out_dir,
+        invert=True,
+        force=True,
+    )
+    assert stats[0]["reads_out"] == 2
+    shutil.rmtree(out_dir, ignore_errors=True)
+
+
+def test_minimap2_reordering_linux():
     stats = lib.clean_paired_fastqs(
         fastqs=[
             (
@@ -579,8 +596,6 @@ def test_invert_paired():
         index=data_dir / "sars-cov-2/sars-cov-2.fasta.gz",
         reorder=True,
         out_dir=out_dir,
-        invert=True,
         force=True,
     )
-    assert stats[0]["reads_out"] == 2
     shutil.rmtree(out_dir, ignore_errors=True)