CHANGES.md

+### Version 2.2.4 - 2019-02-10
+
+  * Fixed bug in --trim5p N which would AdapterRemoval to abort if N was greater
+    than the pre-trimmed read length.
+  * Fixed --identify-adapters not respecting the --mate-separator option.
+
+
 ### Version 2.2.3 - 2019-01-22
 
   * Added support for trimming reads by a fixed amount: --trim5p N --trim3p N.

debian/changelog

+adapterremoval (2.2.4-2) UNRELEASED; urgency=medium
+
+  * d/copyright: Add upstream contact
+
+ -- Andreas Tille <tille@debian.org>  Tue, 05 Mar 2019 11:05:51 +0100
+
+adapterremoval (2.2.4-1) unstable; urgency=medium
+
+  * New upstream pure bugfix release
+  * Run upstream unit tests
+
+ -- Andreas Tille <tille@debian.org>  Thu, 21 Feb 2019 11:22:41 +0100
+
 adapterremoval (2.2.3-1) unstable; urgency=medium
 
   * New upstream version

debian/copyright

 Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: AdapterRemoval
+Upstream-Contact: Mikkel Schubert <mikkelsch@gmail.com>
 Source: https://github.com/MikkelSchubert/adapterremoval/releases
 
 Files: *

debian/rules

@@ -16,7 +16,8 @@ override_dh_auto_build:
 override_dh_auto_test:
 ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	# dh_auto_test
-	echo "*********** Needs adapting to libgtest-dev. ***************"
+	make test
+	make clean_tests
 endif
 
 override_dh_auto_install:

src/debug.cpp

@@ -57,16 +57,17 @@ const char* assert_failed::what() const noexcept
 void debug_raise_assert(const char* filename, size_t lineno, const char* what)
 {
     std::stringstream message;
-    message << "\nFATAL ERROR:\n"
-            << "Debug assertion failed in '" << filename << "', line "
-            << lineno << ": " << what << "\n\n"
-            << "This should not happen! Please file a bug-report at\n    "
-            << "https://github.com/MikkelSchubert/adapterremoval/issues/new";
+    message << "Assertion failed in '" << filename << "', line "
+            << lineno << ": " << what;
 
 #ifdef AR_TEST_BUILD
     throw assert_failed(message.str());
 #else
-    std::cerr << message.str() << std::endl;
+    std::cerr << "\nFATAL ERROR:\n"
+              << message.str() << "\n\n"
+              << "This should not happen! Please file a bug-report at\n    "
+              << "https://github.com/MikkelSchubert/adapterremoval/issues/new"
+              << std::endl;
 
     std::abort();
 #endif

src/debug.hpp

@@ -57,8 +57,8 @@ private:
  * Aborts after printing the filename, line-number, and message, plus
  * instructions for how to report the problem.
  */
-void debug_raise_assert(const char* filename, size_t lineno,
-                        const char* what) __attribute__ ((noreturn));
+[[noreturn]] void debug_raise_assert(const char* filename, size_t lineno,
+                                     const char* what);
 
 
 /** Custom assert which prints various information on failure; always enabled. */

src/fastq.cpp

@@ -244,6 +244,8 @@ fastq::ntrimmed fastq::trim_windowed_bases(const bool trim_ns,
 
 void fastq::truncate(size_t pos, size_t len)
 {
+    AR_DEBUG_ASSERT(pos == 0 || pos <= length());
+
     if (pos || len < length()) {
         m_sequence = m_sequence.substr(pos, len);
         m_qualities = m_qualities.substr(pos, len);

src/fastq_enc.cpp

@@ -36,9 +36,6 @@
 namespace ar
 {
 
-void invalid_solexa(const char offset, const char max_score, const char raw) __attribute__((noreturn));
-
-
 ///////////////////////////////////////////////////////////////////////////////
 // fastq_error
 
@@ -108,7 +105,7 @@ const std::string g_phred_to_solexa = calc_phred_to_solexa();
 
 ///////////////////////////////////////////////////////////////////////////////
 
-void invalid_phred(const char offset, const char max_score, const char raw)
+[[noreturn]] void invalid_phred(const char offset, const char max_score, const char raw)
 {
     if (raw < offset) {
         AR_DEBUG_ASSERT(offset == 33 || offset == 64);
@@ -134,6 +131,8 @@ void invalid_phred(const char offset, const char max_score, const char raw)
                                   "\"--qualitybase solexa\"\n\n"
 
                                   "See README for more information.");
+            } else {
+                AR_DEBUG_FAIL("TODO");
             }
         } else {
             AR_DEBUG_FAIL("Unexpected offset in fastq_encoding::decode");
@@ -181,11 +180,13 @@ void invalid_phred(const char offset, const char max_score, const char raw)
         } else {
             AR_DEBUG_FAIL("Unexpected offset in fastq_encoding::decode");
         }
+    } else {
+        AR_DEBUG_FAIL("invalid_phred called on valid PHRED score");
     }
 }
 
 
-void invalid_solexa(const char offset, const char max_score, const char raw)
+[[noreturn]] void invalid_solexa(const char offset, const char max_score, const char raw)
 {
     if (raw < ';') {
         if (raw < '!') {
@@ -311,7 +312,7 @@ void fastq_encoding_solexa::decode(std::string& qualities) const
     const char max_score = m_offset + m_max_score;
     for (auto& quality : qualities) {
         if (quality < ';' || quality > max_score) {
-            invalid_phred(m_offset, m_max_score, quality);
+            invalid_solexa(m_offset, m_max_score, quality);
         }
 
         quality = g_solexa_to_phred.at(quality - ';') + '!';

src/main.hpp

@@ -31,7 +31,7 @@ namespace ar
 {
 
 const std::string NAME = "AdapterRemoval";
-const std::string VERSION = "ver. 2.2.3";
+const std::string VERSION = "ver. 2.2.4";
 const std::string HELPTEXT = \
     "This program searches for and removes remnant adapter sequences from\n"
     "your read data.  The program can analyze both single end and paired end\n"

src/main_adapter_id.cpp

@@ -414,7 +414,7 @@ private:
                        fastq& read2)
     {
         // Throws if read-names or mate numbering does not match
-        fastq::validate_paired_reads(read1, read2);
+        fastq::validate_paired_reads(read1, read2, m_config.mate_separator);
 
         // Reverse complement to match the orientation of read1
         read2.reverse_complement();

src/main_adapter_rm.cpp

@@ -317,7 +317,11 @@ void trim_read_termini_if_enabled(const userconfig& config, fastq& read, read_ty
     }
 
     if (trim_5p || trim_3p) {
+        if (trim_5p + trim_3p < read.length()) {
             read.truncate(trim_5p, read.length() - std::min(read.length(), trim_5p + trim_3p));
+        } else {
+            read.truncate(0, 0);
+        }
     }
 }
 

tests/regression/misc/trim5p_and_trim3p/pe/trim3p/info.json

+{
+	"arguments": ["--trim3p", "4"],
+	"return_code": 0,
+	"stderr": [
+	]
+}

tests/regression/misc/trim5p_and_trim3p/pe/trim3p/input_1.fastq

+@read_150_158/1
+ATGAGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACCTAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAAAAAAAAAAATAAAAAA
++
+HHHHHHHHFGHHGGFHHDFF;CEEEEGC=@?19@A@<ACDCGFHHHHHHHHHHHHHHHHHHGBDGBE@24A4-EDE35D8DAFFHHEEB;&1''<DBHFC

tests/regression/misc/trim5p_and_trim3p/pe/trim3p/input_2.fastq

+@read_150_158/2
+CATAGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
++
+GIIGHHFHHGCFHHHHHHHHDDB@;B@D?>5BBGBGEBDHHHHHHHHHHGGDDCDEHFHHFHHFFFGHHHHHHBG51?HDEEHHHBFHHHHFDEBEBGFH

tests/regression/misc/trim5p_and_trim3p/pe/trim3p/your_output.discarded

+@read_150_158/1
+
++
+
+@read_150_158/2
+
++
+

tests/regression/misc/trim5p_and_trim3p/pe/trim3p/your_output.settings

+AdapterRemoval ver. 2.2.3
+Trimming of paired-end reads
+
+
+[Adapter sequences]
+Adapter1[1]: AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNATCTCGTATGCCGTCTTCTGCTTG
+Adapter2[1]: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT
+
+
+[Adapter trimming]
+RNG seed: 1695835713
+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: 4
+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: 1
+Number of singleton mate 1 reads: 0
+Number of discarded mate 2 reads: 1
+Number of singleton mate 2 reads: 0
+Number of reads with adapters[1]: 2
+Number of retained reads: 0
+Number of retained nucleotides: 0
+Average length of retained reads: 0
+
+
+[Length distribution]
+Length	Mate1	Mate2	Singleton	Discarded	All
+0	0	0	0	2	2

tests/regression/misc/trim5p_and_trim3p/pe/trim5p/info.json

+{
+	"arguments": ["--trim5p", "4"],
+	"return_code": 0,
+	"stderr": [
+	]
+}