Return a nonzero exit status for detected paired-end read-count mismatches

scripts/test_paired_read_counts.py

@@ -0,0 +1,41 @@
+"""Run: python3 scripts/test_paired_read_counts.py ./fastp (POSIX)."""
+import pathlib
+import subprocess
+import tempfile
+import sys
+
+exe = str(pathlib.Path(sys.argv[1]).resolve())
+failures = 0
+with tempfile.TemporaryDirectory(prefix='fastp-pairs-') as tmp:
+    root = pathlib.Path(tmp)
+    for threads in (1, 4):
+        for n, m, limit in ((999,999,0),(1000,1000,0),(1001,1001,0),
+                            (999,1000,0),(1000,999,0),(1000,1001,0),
+                            (1001,1000,0),(41000,41001,0),(41001,41000,0),
+                            (1000,1001,500)):
+            paths = [root/'r1.fq', root/'r2.fq']
+            for mate, count in enumerate((n,m)):
+                paths[mate].write_text(''.join('@r%d/%d\n%s\n+\n%s\n' %
+                    (i,mate+1,'ACGT'*10,'I'*40) for i in range(count)))
+            cmd = [exe,'-i',str(paths[0]),'-I',str(paths[1]),'-o',str(root/'o1.fq'),
+                   '-O',str(root/'o2.fq'),'-w',str(threads),'-A','-Q','-L','-G',
+                   '--dont_eval_duplication','-j','/dev/null','-h','/dev/null']
+            if limit:
+                cmd += ['--reads_to_process',str(limit)]
+            try:
+                run = subprocess.run(cmd,capture_output=True,timeout=5)
+                if n != m and not limit:
+                    ok = (run.returncode > 0 and
+                          b'Paired-end input files contain different numbers of reads' in run.stderr)
+                else:
+                    expected = limit or n
+                    ok = run.returncode == 0
+                    for mate in (1, 2):
+                        output = root/('o%d.fq' % mate)
+                        ok = ok and output.exists() and output.read_bytes().count(b'\n') == expected*4
+                failures += not ok
+                print('PASS' if ok else 'FAIL',n,m,threads,limit,'exit',run.returncode,flush=True)
+            except subprocess.TimeoutExpired:
+                failures += 1
+                print(n,m,threads,limit,'TIMEOUT',flush=True)
+sys.exit(bool(failures))

src/peprocessor.cpp

@@ -365,8 +365,8 @@ bool PairEndProcessor::processPairEnd(ReadPack* leftPack, ReadPack* rightPack, T
         cerr << "WARNING: different read numbers of the " << mPackProcessedCounter << " pack" << endl;
         cerr << "Read1 pack size: " << leftPack->count << endl;
         cerr << "Read2 pack size: " << rightPack->count << endl;
-        cerr << "Ignore the unmatched reads" << endl << endl;
-        shouldStopReading = true;
+        error_exit("Paired-end input files contain different numbers of reads: "
+            + mOptions->in1 + " and " + mOptions->in2);
     }
     int tid = config->getThreadId();