Fix bug in --adapter-list.

The orientation of mate 2 adapters would not be reversed,
resulting in behavior matching --pcr2 rather than --adapter2.

src/adapterset.cpp

@@ -327,6 +327,7 @@ bool adapter_set::load_adapters(const std::string& filename, bool paired_end)
 
         if (row.second.size() > 1) {
             adapter_3p = row.second.at(1);
+            adapter_3p.reverse_complement();
         }
 
         m_adapters.push_back(fastq_pair(adapter_5p, adapter_3p));

tests/regression/misc/adapter_list/adapters.txt

@@ -0,0 +1 @@
+AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT

tests/regression/misc/adapter_list/info.json

@@ -0,0 +1,6 @@
+{
+	"arguments": ["--adapter-list", "adapters.txt"],
+	"return_code": 0,
+	"stderr": [
+	]
+}

tests/regression/misc/adapter_list/input_1.fastq

@@ -0,0 +1,4 @@
+@AAGGGCSeq_1_5180_50/1 meta data
+ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCTAGATCGGAAGAGCACACGTCTGAACTCCAGTCACAAGGGCATCTCGTATG
++
+IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECCBCCBCBEBCDBABABA?A@?@?>==>==<><<:<996978544100-,)!

tests/regression/misc/adapter_list/input_2.fastq

@@ -0,0 +1,4 @@
+@AAGGGCSeq_1_5180_50/2 data meta
+AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGTAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC
++
+JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDEDBDBCBCCBBAA?ADAAA@@@>>>><=><<;<:<;87:78753420/,+)!

tests/regression/misc/adapter_list/your_output.pair1.truncated

@@ -0,0 +1,4 @@
+@AAGGGCSeq_1_5180_50/1 meta data
+ACATGACTAACACCCTTAATTCCATCCACCCTCCTCTCCCTAGCAGGCCT
++
+IJJHJJIJIIHJHHIGIHIGGGIGFGEFGGFGGEHGFHGFEDFFFEDECC

tests/regression/misc/adapter_list/your_output.pair2.truncated

@@ -0,0 +1,4 @@
+@AAGGGCSeq_1_5180_50/2 data meta
+AGGCCTCCTAGGGAGAGGAGGGTGGATGGAATTAAGGGTGTTAGTCATGT
++
+JIHJJIJJJJJIHIHJHJHHJFGIHHHGHGGEGFIHEEDEEFBEDFEDED

tests/regression/misc/adapter_list/your_output.settings

@@ -0,0 +1,96 @@
+AdapterRemoval ver. 2.1.7
+Trimming of paired-end reads
+
+
+[Adapter sequences]
+Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG
+Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
+
+
+[Adapter trimming]
+RNG seed: 372265332
+Alignment shift value: 2
+Global mismatch threshold: 0.333333
+Quality format (input): Phred+33
+Quality score max (input): 41
+Quality format (output): Phred+33
+Quality score max (output): 41
+Mate-number separator (input): '/'
+Trimming 5p: 0
+Trimming 3p: 0
+Trimming Ns: No
+Trimming Phred scores <= 2: No
+Trimming using sliding windows: No
+Minimum genomic length: 15
+Maximum genomic length: 4294967295
+Collapse overlapping reads: No
+Minimum overlap (in case of collapse): 11
+
+
+[Trimming statistics]
+Total number of read pairs: 1
+Number of unaligned read pairs: 0
+Number of well aligned read pairs: 1
+Number of discarded mate 1 reads: 0
+Number of singleton mate 1 reads: 0
+Number of discarded mate 2 reads: 0
+Number of singleton mate 2 reads: 0
+Number of reads with adapters[1]: 2
+Number of retained reads: 2
+Number of retained nucleotides: 100
+Average length of retained reads: 50
+
+
+[Length distribution]
+Length	Mate1	Mate2	Singleton	Discarded	All
+0	0	0	0	0	0
+1	0	0	0	0	0
+2	0	0	0	0	0
+3	0	0	0	0	0
+4	0	0	0	0	0
+5	0	0	0	0	0
+6	0	0	0	0	0
+7	0	0	0	0	0
+8	0	0	0	0	0
+9	0	0	0	0	0
+10	0	0	0	0	0
+11	0	0	0	0	0
+12	0	0	0	0	0
+13	0	0	0	0	0
+14	0	0	0	0	0
+15	0	0	0	0	0
+16	0	0	0	0	0
+17	0	0	0	0	0
+18	0	0	0	0	0
+19	0	0	0	0	0
+20	0	0	0	0	0
+21	0	0	0	0	0
+22	0	0	0	0	0
+23	0	0	0	0	0
+24	0	0	0	0	0
+25	0	0	0	0	0
+26	0	0	0	0	0
+27	0	0	0	0	0
+28	0	0	0	0	0
+29	0	0	0	0	0
+30	0	0	0	0	0
+31	0	0	0	0	0
+32	0	0	0	0	0
+33	0	0	0	0	0
+34	0	0	0	0	0
+35	0	0	0	0	0
+36	0	0	0	0	0
+37	0	0	0	0	0
+38	0	0	0	0	0
+39	0	0	0	0	0
+40	0	0	0	0	0
+41	0	0	0	0	0
+42	0	0	0	0	0
+43	0	0	0	0	0
+44	0	0	0	0	0
+45	0	0	0	0	0
+46	0	0	0	0	0
+47	0	0	0	0	0
+48	0	0	0	0	0
+49	0	0	0	0	0
+50	1	1	0	0	2

tests/regression/run

@@ -243,6 +243,10 @@ class TestCase(object):
             with open(os.path.join(root, 'barcodes.txt'), 'w') as handle:
                 handle.writelines(self._files['barcodes'])
 
+        if 'adapters' in self._files:
+            with open(os.path.join(root, 'adapters.txt'), 'w') as handle:
+                handle.writelines(self._files['adapters'])
+
         return final_files["input_1"], final_files["input_2"]
 
     def _do_call(self, root, input_1, input_2, compression, interleaved):
@@ -278,13 +282,14 @@ class TestCase(object):
 
     def _check_file_creation(self, root, input_1, input_2, compression):
         expected_files = set(self._files["output"])
-        if 'barcodes' in self._files:
-            expected_files.add('barcodes.txt')
+        for key in ('barcodes', 'adapters'):
+            if key in self._files:
+                expected_files.add(key + '.txt')
 
         if compression != UNCOMPRESSED:
             expected_files_ = set()
             for value in expected_files:
-                if not value.endswith(".settings") and value != 'barcodes.txt':
+                if not (value.endswith(".settings") or value.endswith(".txt")):
                     expected_files_.add(value + "." + compression)
                 else:
                     expected_files_.add(value)
@@ -391,10 +396,12 @@ class TestCase(object):
                 result["input_1"].append(os.path.join(abs_root, filename))
             elif filename.startswith("input_2"):
                 result["input_2"].append(os.path.join(abs_root, filename))
-            elif filename not in ('info.json', 'README', 'barcodes.txt'):
-                result["output"][filename] = read_lines(root, filename)
             elif filename == 'barcodes.txt':
                 result["barcodes"] = read_lines(root, filename)
+            elif filename == 'adapters.txt':
+                result["adapters"] = read_lines(root, filename)
+            elif filename not in ('info.json', 'README'):
+                result["output"][filename] = read_lines(root, filename)
 
         return result