Merge pull request #160 from rhpvorderman/issue159

Fix issue with FASTQ files without adapters causing crashes for the insert size metrics module.

Author: rhpvorderman

CHANGELOG.rst

@@ -7,6 +7,11 @@ Changelog
 .. This document is user facing. Please word the changes in such a way
 .. that users understand how the changes affect the new version.
 
+version 0.9.1
+-----------------
++ Fix an issue where the insert size metrics module would crash when no
+  adapters where present.
+
 version 0.9.0
 -----------------
 + MultiQC support since MultiQC version 1.22

src/sequali/report_modules.py

@@ -1843,8 +1843,8 @@ def from_insert_size_metrics(cls, metrics: InsertSizeMetrics):
                 metrics.adapters_read1())
         adapters_read2 = AdapterFromOverlapReport.select_relevant_adapters(
             metrics.adapters_read2())
-        longest_adapter_read1 = adapters_read1[-1][0]
-        longest_adapter_read2 = adapters_read2[-1][0]
+        longest_adapter_read1 = adapters_read1[-1][0] if adapters_read1 else ""
+        longest_adapter_read2 = adapters_read2[-1][0] if adapters_read2 else ""
         longest_adapter_read1_match = identify_sequence_builtin(
             longest_adapter_read1)[2]
         longest_adapter_read2_match = identify_sequence_builtin(

tests/test_integration.py

@@ -51,6 +51,19 @@ def test_empty_file(tmp_path):
     assert result["summary"]["total_bases"] == 0
 
 
+def test_empty_file_paired(tmp_path):
+    empty_fastq = TEST_DATA / "empty.fastq"
+    sys.argv = ["", "--dir", str(tmp_path), str(empty_fastq), str(empty_fastq)]
+    main()
+    simple_fastq_json = tmp_path / "empty.fastq.json"
+    assert simple_fastq_json.exists()
+    result = json.loads(simple_fastq_json.read_text())
+    assert result["summary_read2"]["maximum_length"] == 0
+    assert result["summary_read2"]["minimum_length"] == 0
+    assert result["summary_read2"]["total_gc_bases"] == 0
+    assert result["summary_read2"]["total_bases"] == 0
+
+
 def test_empty_read(tmp_path):
     empty_read_fastq = TEST_DATA / "empty_read.fastq"
     sys.argv = ["", "--dir", str(tmp_path), str(empty_read_fastq)]
@@ -64,6 +77,20 @@ def test_empty_read(tmp_path):
     assert result["summary"]["total_bases"] == 0
 
 
+def test_empty_read_paired(tmp_path):
+    empty_read_fastq = TEST_DATA / "empty_read.fastq"
+    sys.argv = ["", "--dir", str(tmp_path), str(empty_read_fastq),
+                str(empty_read_fastq)]
+    main()
+    simple_fastq_json = tmp_path / "empty_read.fastq.json"
+    assert simple_fastq_json.exists()
+    result = json.loads(simple_fastq_json.read_text())
+    assert result["summary_read2"]["maximum_length"] == 0
+    assert result["summary_read2"]["minimum_length"] == 0
+    assert result["summary_read2"]["total_gc_bases"] == 0
+    assert result["summary_read2"]["total_bases"] == 0
+
+
 def test_adapters_only(tmp_path):
     adapters_fastq = TEST_DATA / "100_illumina_adapters.fastq"
     sys.argv = ["", "--dir", str(tmp_path),