Return a nonzero exit status for detected FASTQ parsing errors

scripts/test_fastq_parse_errors.py

@@ -0,0 +1,55 @@
+#!/usr/bin/env python3
+"""Run: python3 scripts/test_fastq_parse_errors.py ./fastp."""
+import gzip
+import pathlib
+import subprocess
+import sys
+import tempfile
+
+
+def main():
+    exe = str(pathlib.Path(sys.argv[1]).resolve())
+    record = b'@valid\nACGTACGTACGTACGTACGT\n+\nIIIIIIIIIIIIIIIIIIII\n'
+    # Place errors beyond initial sampling as well as at the first record.
+    cases = [
+        ('valid', record*4, None),
+        ('no_final_newline', (record*4).rstrip(b'\n'), None),
+        ('invalid_separator', b'@bad\nACGT\nwrong\nIIII\n', 'Invalid FASTQ separator'),
+        ('missing_separator', b'@bad\nACGT\n', 'Invalid FASTQ separator'),
+        ('short_quality', b'@bad\nACGT\n+\nIII\n', 'FASTQ sequence/quality length mismatch'),
+        ('long_quality', b'@bad\nACGT\n+\nIIIII\n', 'FASTQ sequence/quality length mismatch'),
+        ('missing_quality', b'@bad\nACGT\n+\n', 'FASTQ sequence/quality length mismatch'),
+    ]
+    failures = 0
+    with tempfile.TemporaryDirectory(prefix='fastp-parse-test-') as tmp:
+        root = pathlib.Path(tmp)
+        for zipped in (False, True):
+            for name, data, expected_error in cases:
+                for late in ((False, True) if expected_error else (False,)):
+                    label = '%s-%s-%s' % (name, zipped, late)
+                    content = record*40000 + data if late else data
+                    source = root/(label + ('.fq.gz' if zipped else '.fq'))
+                    output = root/(label+'.out.fq')
+                    source.write_bytes(gzip.compress(content) if zipped else content)
+                    cmd = [exe, '-i', str(source), '-o', str(output), '-w', '2',
+                           '-A', '-Q', '-L', '-G', '--dont_eval_duplication',
+                           '-j', '/dev/null', '-h', '/dev/null']
+                    try:
+                        run = subprocess.run(cmd, capture_output=True, timeout=30)
+                        if expected_error:
+                            ok = (run.returncode > 0 and
+                                  expected_error.encode() in run.stderr and
+                                  str(source).encode() in run.stderr)
+                        else:
+                            ok = (run.returncode == 0 and output.exists() and
+                                  output.read_bytes() == content.rstrip(b'\n')+b'\n')
+                        detail = 'exit=%d' % run.returncode
+                    except subprocess.TimeoutExpired:
+                        ok, detail = False, 'timeout'
+                    print('%s %s %s' % ('PASS' if ok else 'FAIL', label, detail))
+                    failures += not ok
+    return bool(failures)
+
+
+if __name__ == '__main__':
+    sys.exit(main())

src/fastqreader.cpp

@@ -347,8 +347,7 @@ Read* FastqReader::read(){
 	if (strand->empty() || (*strand)[0]!='+') {
 		cerr << *name << endl;
 		cerr << "Expected '+', got " << *strand << endl;
-		cerr << "Your FASTQ may be invalid, please check the tail of your FASTQ file" << endl;
-		return NULL;
+		error_exit("Invalid FASTQ separator in: " + mFilename);
 	}
 
 	if(quality->length() != sequence->length()) {
@@ -357,8 +356,7 @@ Read* FastqReader::read(){
 		cerr << *sequence << endl;
 		cerr << *strand << endl;
 		cerr << *quality << endl;
-		cerr << "Your FASTQ may be invalid, please check the tail of your FASTQ file" << endl;
-		return NULL;
+		error_exit("FASTQ sequence/quality length mismatch in: " + mFilename);
 	}
 
 	if(readInPool)