Fix OutputFileWriter crash when produce_fastq=false and only BAM outp…

neat/read_simulator/utils/output_file_writer.py

@@ -117,7 +117,7 @@ def __init__(self,
         self.vcf = vcf
         self.bam = bam
 
-        if not file_handles:
+        if not file_handles and self.bam is None:
             _LOG.error("output_file_writer received no files!")
             raise ValueError
 

tests/test_read_simulator/test_output_file_writer.py

@@ -124,6 +124,42 @@ def test_ofw_no_files_raises(tmp_path):
         OutputFileWriter(options=opts)
 
 
+def test_ofw_bam_only_with_header_is_accepted(tmp_path):
+    """BAM-only (no FASTQ, no VCF) with a bam_header opens the BAM handle."""
+    opts = _make_options(tmp_path, fq1=False, bam=True,
+                         produce_fastq=False, produce_bam=True)
+    ofw = OutputFileWriter(options=opts, bam_header={"chr1": 1000})
+    assert ofw.bam is not None
+    assert ofw.bam in ofw.files_to_write
+    assert ofw.fq1 is None
+    assert ofw.vcf is None
+    ofw.flush_and_close_files()
+
+
+def test_ofw_bam_only_no_header_is_accepted(tmp_path):
+    """BAM-only with bam_header=None (the runner's path) must not raise.
+    pysam manages the merged output file so no handle is opened here."""
+    opts = _make_options(tmp_path, fq1=False, bam=True,
+                         produce_fastq=False, produce_bam=True)
+    ofw = OutputFileWriter(options=opts, bam_header=None)
+    assert ofw.bam is not None
+    assert ofw.fq1 is None
+    assert ofw.vcf is None
+    assert ofw.bam not in ofw.files_to_write
+
+
+def test_ofw_vcf_only_is_accepted(tmp_path):
+    """VCF-only (no FASTQ, no BAM) should construct without error."""
+    opts = _make_options(tmp_path, fq1=False, vcf=True,
+                         produce_fastq=False, produce_vcf=True)
+    ofw = OutputFileWriter(options=opts, vcf_header={"chr1": 1000})
+    assert ofw.vcf is not None
+    assert ofw.vcf in ofw.files_to_write
+    assert ofw.fq1 is None
+    assert ofw.bam is None
+    ofw.flush_and_close_files()
+
+
 def test_ofw_fq1_is_none_when_not_requested(tmp_path):
     ofw = _make_ofw(tmp_path, fq1=True)
     assert ofw.fq2 is None

tests/test_read_simulator/test_runner.py

@@ -415,3 +415,47 @@ def test_runner_with_produce_bam(tmp_path):
     read_simulator_runner(str(cfg), str(out_dir), "test")
     bam_files = list(out_dir.glob("*.bam"))
     assert len(bam_files) >= 1, "Expected at least one BAM output file"
+
+
+def test_runner_bam_only_no_fastq(tmp_path):
+    """produce_bam=true + produce_fastq=false must write a BAM and no FASTQ."""
+    ref = _write_ref(tmp_path / "ref.fa")
+    cfg = _write_config(
+        tmp_path / "conf.yml", ref,
+        produce_fastq="false",
+        produce_bam="true",
+    )
+    out_dir = tmp_path / "out"
+    read_simulator_runner(str(cfg), str(out_dir), "test")
+    assert list(out_dir.glob("*.bam")), "Expected a BAM output file"
+    assert not list(out_dir.glob("*.fastq.gz")), "Expected no FASTQ output"
+
+
+def test_runner_vcf_only_no_fastq(tmp_path):
+    """produce_vcf=true + produce_fastq=false must write a VCF and no FASTQ."""
+    ref = _write_ref(tmp_path / "ref.fa")
+    cfg = _write_config(
+        tmp_path / "conf.yml", ref,
+        produce_fastq="false",
+        produce_vcf="true",
+    )
+    out_dir = tmp_path / "out"
+    read_simulator_runner(str(cfg), str(out_dir), "test")
+    assert list(out_dir.glob("*.vcf.gz")), "Expected a VCF output file"
+    assert not list(out_dir.glob("*.fastq.gz")), "Expected no FASTQ output"
+
+
+def test_runner_bam_and_vcf_no_fastq(tmp_path):
+    """produce_bam=true + produce_vcf=true + produce_fastq=false must write both."""
+    ref = _write_ref(tmp_path / "ref.fa")
+    cfg = _write_config(
+        tmp_path / "conf.yml", ref,
+        produce_fastq="false",
+        produce_bam="true",
+        produce_vcf="true",
+    )
+    out_dir = tmp_path / "out"
+    read_simulator_runner(str(cfg), str(out_dir), "test")
+    assert list(out_dir.glob("*.bam")), "Expected a BAM output file"
+    assert list(out_dir.glob("*.vcf.gz")), "Expected a VCF output file"
+    assert not list(out_dir.glob("*.fastq.gz")), "Expected no FASTQ output"