Commit 5eb60d22 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 2.2.4

parent 34df23e4

CHANGES.md

+7 −0
Original line number Diff line number Diff line 
### 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.

src/debug.cpp

+7 −6
Original line number Diff line number Diff line
@@ -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

+2 −2
Original line number Diff line number Diff line
@@ -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

+2 −0
Original line number Diff line number Diff line
@@ -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

+7 −6
Original line number Diff line number Diff line
@@ -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 - ';') + '!';