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commit 00cf2a2de2070b110c6d464c6b216066839966f3 Author: Kevin Murray <[email protected]> Date: Thu Sep 24 17:21:44 2015 +1000 Imported Upstream version 2.4.0+dfsg --- CMakeLists.txt | 2 +- docs/Doxyfile | 2 +- src/api/BamAlignment.h | 8 ++++---- src/api/BamAux.h | 6 ++++++ src/api/BamReader.cpp | 6 +++--- src/api/BamWriter.h | 2 +- src/api/CMakeLists.txt | 2 +- src/api/SamHeader.cpp | 2 ++ src/api/SamHeader.h | 3 +++ src/api/SamProgram.cpp | 1 + src/api/SamProgram.h | 2 ++ src/api/SamReadGroup.cpp | 2 ++ src/api/SamReadGroup.h | 3 +++ src/api/SamSequence.cpp | 2 ++ src/api/SamSequence.h | 3 +++ src/api/internal/io/HostAddress_p.cpp | 2 +- src/api/internal/io/HttpHeader_p.cpp | 3 +-- src/api/internal/io/TcpSocketEngine_p.h | 2 +- src/api/internal/sam/SamFormatParser_p.cpp | 24 ++++++++++++++++++++++ src/api/internal/sam/SamFormatParser_p.h | 2 +- src/api/internal/sam/SamFormatPrinter_p.cpp | 31 +++++++++++++++++++++++++++++ src/api/internal/sam/SamFormatPrinter_p.h | 2 +- src/api/internal/sam/SamHeaderValidator_p.h | 6 +++--- src/toolkit/CMakeLists.txt | 2 +- src/toolkit/bamtools.cpp | 2 +- src/toolkit/bamtools_filter.h | 2 +- src/toolkit/bamtools_resolve.cpp | 2 -- src/toolkit/bamtools_sort.h | 2 +- src/toolkit/bamtools_split.h | 2 +- src/utils/bamtools_fasta.cpp | 2 +- 30 files changed, 104 insertions(+), 28 deletions(-) diff --git a/CMakeLists.txt b/CMakeLists.txt index 9b97fa0..dade1e3 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -31,7 +31,7 @@ ensure_out_of_source_build( " # set BamTools version information set( BamTools_VERSION_MAJOR 2 ) -set( BamTools_VERSION_MINOR 3 ) +set( BamTools_VERSION_MINOR 4 ) set( BamTools_VERSION_BUILD 0 ) # set our library and executable destination dirs diff --git a/docs/Doxyfile b/docs/Doxyfile index 410ea27..7c21624 100644 --- a/docs/Doxyfile +++ b/docs/Doxyfile @@ -31,7 +31,7 @@ PROJECT_NAME = BamTools # This could be handy for archiving the generated documentation or # if some version control system is used. -PROJECT_NUMBER = 2.3.0 +PROJECT_NUMBER = 2.4.0 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) # base path where the generated documentation will be put. diff --git a/src/api/BamAlignment.h b/src/api/BamAlignment.h index e12aad6..d5eda4f 100644 --- a/src/api/BamAlignment.h +++ b/src/api/BamAlignment.h @@ -2,7 +2,7 @@ // BamAlignment.h (c) 2009 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 4 December 2012 (DB) +// Last modified: 25 July 2013 (DB) // --------------------------------------------------------------------------- // Provides the BamAlignment data structure // *************************************************************************** @@ -29,7 +29,7 @@ namespace Internal { //! \endcond // BamAlignment data structure -struct API_EXPORT BamAlignment { +class API_EXPORT BamAlignment { // constructors & destructor public: @@ -116,8 +116,8 @@ struct API_EXPORT BamAlignment { public: std::string Name; // read name int32_t Length; // length of query sequence - std::string QueryBases; // 'original' sequence (as reported from sequencing machine) - std::string AlignedBases; // 'aligned' sequence (includes any indels, padding, clipping) + std::string QueryBases; // 'original' sequence (contained in BAM file) + std::string AlignedBases; // 'aligned' sequence (QueryBases plus deletion, padding, clipping chars) std::string Qualities; // FASTQ qualities (ASCII characters, not numeric values) std::string TagData; // tag data (use provided methods to query/modify) int32_t RefID; // ID number for reference sequence diff --git a/src/api/BamAux.h b/src/api/BamAux.h index 0dd3e99..b448b76 100644 --- a/src/api/BamAux.h +++ b/src/api/BamAux.h @@ -133,6 +133,12 @@ struct API_EXPORT BamRegion { } }; +struct CustomHeaderTag { + std::string TagName; + std::string TagValue; +}; + + // ---------------------------------------------------------------- // General utility methods diff --git a/src/api/BamReader.cpp b/src/api/BamReader.cpp index 0728d96..c4f0432 100644 --- a/src/api/BamReader.cpp +++ b/src/api/BamReader.cpp @@ -2,7 +2,7 @@ // BamReader.cpp (c) 2009 Derek Barnett, Michael Str�mberg // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- -// Last modified: 18 November 2012 (DB) +// Last modified: 29 July 2013 (DB) // --------------------------------------------------------------------------- // Provides read access to BAM files. // *************************************************************************** @@ -171,8 +171,8 @@ bool BamReader::GetNextAlignment(BamAlignment& alignment) { However, this method does NOT populate the alignment's string data fields (read name, bases, qualities, tags, filename). This provides a boost in speed - when these fields are not required for every alignment. These fields can be - populated 'lazily' (as needed) by calling BamAlignment::BuildCharData() later. + when these fields are not required for every alignment. These fields, excluding filename, + can be populated 'lazily' (as needed) by calling BamAlignment::BuildCharData() later. \param[out] alignment destination for alignment record data \returns \c true if a valid alignment was found diff --git a/src/api/BamWriter.h b/src/api/BamWriter.h index 68257ee..f481721 100644 --- a/src/api/BamWriter.h +++ b/src/api/BamWriter.h @@ -17,7 +17,7 @@ namespace BamTools { class BamAlignment; -class SamHeader; +struct SamHeader; //! \cond namespace Internal { diff --git a/src/api/CMakeLists.txt b/src/api/CMakeLists.txt index 7e3d3ca..32edcff 100644 --- a/src/api/CMakeLists.txt +++ b/src/api/CMakeLists.txt @@ -34,7 +34,7 @@ set( BamToolsAPISources # create main BamTools API shared library add_library( BamTools SHARED ${BamToolsAPISources} ) set_target_properties( BamTools PROPERTIES - SOVERSION "2.3.0" + SOVERSION "2.4.0" OUTPUT_NAME "bamtools" ) # create main BamTools API static library diff --git a/src/api/SamHeader.cpp b/src/api/SamHeader.cpp index 9221944..09635a6 100644 --- a/src/api/SamHeader.cpp +++ b/src/api/SamHeader.cpp @@ -69,6 +69,7 @@ SamHeader::SamHeader(const SamHeader& other) : Version(other.Version) , SortOrder(other.SortOrder) , GroupOrder(other.GroupOrder) + , CustomTags(other.CustomTags) , Sequences(other.Sequences) , ReadGroups(other.ReadGroups) , Programs(other.Programs) @@ -90,6 +91,7 @@ void SamHeader::Clear(void) { Version.clear(); SortOrder.clear(); GroupOrder.clear(); + CustomTags.clear(); Sequences.Clear(); ReadGroups.Clear(); Programs.Clear(); diff --git a/src/api/SamHeader.h b/src/api/SamHeader.h index 5004994..51a66e3 100644 --- a/src/api/SamHeader.h +++ b/src/api/SamHeader.h @@ -11,6 +11,7 @@ #define SAM_HEADER_H #include "api/api_global.h" +#include "api/BamAux.h" #include "api/SamProgramChain.h" #include "api/SamReadGroupDictionary.h" #include "api/SamSequenceDictionary.h" @@ -19,6 +20,7 @@ namespace BamTools { + struct API_EXPORT SamHeader { // ctor & dtor @@ -51,6 +53,7 @@ struct API_EXPORT SamHeader { std::string Version; // VN:<Version> *Required, if @HD record is present* std::string SortOrder; // SO:<SortOrder> std::string GroupOrder; // GO:<GroupOrder> + std::vector<CustomHeaderTag> CustomTags; // optional custom tags on @HD line // header sequences (@SQ entries) SamSequenceDictionary Sequences; diff --git a/src/api/SamProgram.cpp b/src/api/SamProgram.cpp index 1720678..340988f 100644 --- a/src/api/SamProgram.cpp +++ b/src/api/SamProgram.cpp @@ -75,6 +75,7 @@ SamProgram::SamProgram(const SamProgram& other) , Name(other.Name) , PreviousProgramID(other.PreviousProgramID) , Version(other.Version) + , CustomTags(other.CustomTags) , NextProgramID(other.NextProgramID) { } diff --git a/src/api/SamProgram.h b/src/api/SamProgram.h index 54da872..41fd303 100644 --- a/src/api/SamProgram.h +++ b/src/api/SamProgram.h @@ -11,6 +11,7 @@ #define SAM_PROGRAM_H #include "api/api_global.h" +#include "api/BamAux.h" #include <string> namespace BamTools { @@ -41,6 +42,7 @@ struct API_EXPORT SamProgram { std::string Name; // PN:<Name> std::string PreviousProgramID; // PP:<PreviousProgramID> std::string Version; // VN:<Version> + std::vector<CustomHeaderTag> CustomTags; // optional custom tags // internal (non-standard) methods & fields private: diff --git a/src/api/SamReadGroup.cpp b/src/api/SamReadGroup.cpp index ce022ab..8f0f7e7 100644 --- a/src/api/SamReadGroup.cpp +++ b/src/api/SamReadGroup.cpp @@ -111,6 +111,7 @@ SamReadGroup::SamReadGroup(const SamReadGroup& other) , Sample(other.Sample) , SequencingCenter(other.SequencingCenter) , SequencingTechnology(other.SequencingTechnology) + , CustomTags(other.CustomTags) { } /*! \fn SamReadGroup::~SamReadGroup(void) @@ -134,6 +135,7 @@ void SamReadGroup::Clear(void) { Sample.clear(); SequencingCenter.clear(); SequencingTechnology.clear(); + CustomTags.clear(); } /*! \fn bool SamReadGroup::HasDescription(void) const diff --git a/src/api/SamReadGroup.h b/src/api/SamReadGroup.h index 093ce2d..d3699c8 100644 --- a/src/api/SamReadGroup.h +++ b/src/api/SamReadGroup.h @@ -11,7 +11,9 @@ #define SAM_READGROUP_H #include "api/api_global.h" +#include "api/BamAux.h" #include <string> +#include <vector> namespace BamTools { @@ -54,6 +56,7 @@ struct API_EXPORT SamReadGroup { std::string Sample; // SM:<Sample> std::string SequencingCenter; // CN:<SequencingCenter> std::string SequencingTechnology; // PL:<SequencingTechnology> + std::vector<CustomHeaderTag> CustomTags; // optional custom tags }; /*! \fn bool operator==(const SamReadGroup& lhs, const SamReadGroup& rhs) diff --git a/src/api/SamSequence.cpp b/src/api/SamSequence.cpp index dea176b..f3d07d9 100644 --- a/src/api/SamSequence.cpp +++ b/src/api/SamSequence.cpp @@ -99,6 +99,7 @@ SamSequence::SamSequence(const SamSequence& other) , Name(other.Name) , Species(other.Species) , URI(other.URI) + , CustomTags(other.CustomTags) { } /*! \fn SamSequence::~SamSequence(void) @@ -116,6 +117,7 @@ void SamSequence::Clear(void) { Name.clear(); Species.clear(); URI.clear(); + CustomTags.clear(); } /*! \fn bool SamSequence::HasAssemblyID(void) const diff --git a/src/api/SamSequence.h b/src/api/SamSequence.h index c1a8792..27dc507 100644 --- a/src/api/SamSequence.h +++ b/src/api/SamSequence.h @@ -11,7 +11,9 @@ #define SAM_SEQUENCE_H #include "api/api_global.h" +#include "api/BamAux.h" #include <string> +#include <vector> namespace BamTools { @@ -42,6 +44,7 @@ struct API_EXPORT SamSequence { std::string Name; // SN:<Name> *Required for valid SAM header* std::string Species; // SP:<Species> std::string URI; // UR:<URI> + std::vector<CustomHeaderTag> CustomTags; // optional custom tags }; /*! \fn bool operator==(const SamSequence& lhs, const SamSequence& rhs) diff --git a/src/api/internal/io/HostAddress_p.cpp b/src/api/internal/io/HostAddress_p.cpp index 5c42c5b..1b4e57d 100644 --- a/src/api/internal/io/HostAddress_p.cpp +++ b/src/api/internal/io/HostAddress_p.cpp @@ -263,7 +263,7 @@ bool HostAddress::operator<(const HostAddress& other) const { // if self is IPv4 if ( m_protocol == HostAddress::IPv4Protocol ) { if ( other.m_protocol == HostAddress::IPv4Protocol ) - return m_ip4Address < m_ip4Address; + return m_ip4Address < other.m_ip4Address; } // if self is IPv6 diff --git a/src/api/internal/io/HttpHeader_p.cpp b/src/api/internal/io/HttpHeader_p.cpp index 156df26..fa71886 100644 --- a/src/api/internal/io/HttpHeader_p.cpp +++ b/src/api/internal/io/HttpHeader_p.cpp @@ -1,4 +1,4 @@ -// *************************************************************************** +// *************************************************************************** // HttpHeader_p.cpp (c) 2011 Derek Barnett // Marth Lab, Department of Biology, Boston College // --------------------------------------------------------------------------- @@ -30,7 +30,6 @@ static const char COLON_CHAR = ':'; static const char DOT_CHAR = '.'; static const char NEWLINE_CHAR = '\n'; static const char SPACE_CHAR = ' '; -static const char TAB_CHAR = '\t'; static const string FIELD_NEWLINE = "\r\n"; static const string FIELD_SEPARATOR = ": "; diff --git a/src/api/internal/io/TcpSocketEngine_p.h b/src/api/internal/io/TcpSocketEngine_p.h index 9218278..a315334 100644 --- a/src/api/internal/io/TcpSocketEngine_p.h +++ b/src/api/internal/io/TcpSocketEngine_p.h @@ -30,7 +30,7 @@ namespace BamTools { namespace Internal { -struct TcpSocketEngine { +class TcpSocketEngine { // ctors & dtor public: diff --git a/src/api/internal/sam/SamFormatParser_p.cpp b/src/api/internal/sam/SamFormatParser_p.cpp index 928cb5c..0a2d085 100644 --- a/src/api/internal/sam/SamFormatParser_p.cpp +++ b/src/api/internal/sam/SamFormatParser_p.cpp @@ -74,6 +74,12 @@ void SamFormatParser::ParseHDLine(const string& line) { if ( tokenTag == Constants::SAM_HD_VERSION_TAG ) m_header.Version = tokenValue; else if ( tokenTag == Constants::SAM_HD_SORTORDER_TAG ) m_header.SortOrder = tokenValue; else if ( tokenTag == Constants::SAM_HD_GROUPORDER_TAG ) m_header.GroupOrder = tokenValue; + else { // custom tag + CustomHeaderTag otherTag; + otherTag.TagName = tokenTag; + otherTag.TagValue = tokenValue; + m_header.CustomTags.push_back(otherTag); + } } // check for required tags @@ -104,6 +110,12 @@ void SamFormatParser::ParseSQLine(const string& line) { else if ( tokenTag == Constants::SAM_SQ_CHECKSUM_TAG ) seq.Checksum = tokenValue; else if ( tokenTag == Constants::SAM_SQ_SPECIES_TAG ) seq.Species = tokenValue; else if ( tokenTag == Constants::SAM_SQ_URI_TAG ) seq.URI = tokenValue; + else { // custom tag + CustomHeaderTag otherTag; + otherTag.TagName = tokenTag; + otherTag.TagValue = tokenValue; + seq.CustomTags.push_back(otherTag); + } } // check for required tags @@ -145,6 +157,12 @@ void SamFormatParser::ParseRGLine(const string& line) { else if ( tokenTag == Constants::SAM_RG_SAMPLE_TAG ) rg.Sample = tokenValue; else if ( tokenTag == Constants::SAM_RG_SEQCENTER_TAG ) rg.SequencingCenter = tokenValue; else if ( tokenTag == Constants::SAM_RG_SEQTECHNOLOGY_TAG ) rg.SequencingTechnology = tokenValue; + else { // custom tag + CustomHeaderTag otherTag; + otherTag.TagName = tokenTag; + otherTag.TagValue = tokenValue; + rg.CustomTags.push_back(otherTag); + } } // check for required tags @@ -177,6 +195,12 @@ void SamFormatParser::ParsePGLine(const string& line) { else if ( tokenTag == Constants::SAM_PG_COMMANDLINE_TAG ) pg.CommandLine = tokenValue; else if ( tokenTag == Constants::SAM_PG_PREVIOUSPROGRAM_TAG ) pg.PreviousProgramID = tokenValue; else if ( tokenTag == Constants::SAM_PG_VERSION_TAG ) pg.Version = tokenValue; + else { // custom tag + CustomHeaderTag otherTag; + otherTag.TagName = tokenTag; + otherTag.TagValue = tokenValue; + pg.CustomTags.push_back(otherTag); + } } // check for required tags diff --git a/src/api/internal/sam/SamFormatParser_p.h b/src/api/internal/sam/SamFormatParser_p.h index cf6d54c..ffe0b3b 100644 --- a/src/api/internal/sam/SamFormatParser_p.h +++ b/src/api/internal/sam/SamFormatParser_p.h @@ -25,7 +25,7 @@ namespace BamTools { -class SamHeader; +struct SamHeader; namespace Internal { diff --git a/src/api/internal/sam/SamFormatPrinter_p.cpp b/src/api/internal/sam/SamFormatPrinter_p.cpp index 5a51a2f..9aebb99 100644 --- a/src/api/internal/sam/SamFormatPrinter_p.cpp +++ b/src/api/internal/sam/SamFormatPrinter_p.cpp @@ -70,6 +70,13 @@ void SamFormatPrinter::PrintHD(std::stringstream& out) const { if ( m_header.HasGroupOrder() ) out << FormatTag(Constants::SAM_HD_GROUPORDER_TAG, m_header.GroupOrder); + // custom tags + if ( !m_header.CustomTags.empty() ) { + for (size_t i = 0; i < m_header.CustomTags.size(); ++i) { + const CustomHeaderTag& customTag = m_header.CustomTags[i]; + out << FormatTag(customTag.TagName, customTag.TagValue); + } + } // newline out << endl; } @@ -104,6 +111,14 @@ void SamFormatPrinter::PrintSQ(std::stringstream& out) const { if ( seq.HasURI() ) out << FormatTag(Constants::SAM_SQ_URI_TAG, seq.URI); + // custom tags + if ( !seq.CustomTags.empty() ) { + for (size_t i = 0; i < seq.CustomTags.size(); ++i) { + const CustomHeaderTag& customTag = seq.CustomTags[i]; + out << FormatTag(customTag.TagName, customTag.TagValue); + } + } + // newline out << endl; } @@ -165,6 +180,14 @@ void SamFormatPrinter::PrintRG(std::stringstream& out) const { if ( rg.HasSample() ) out << FormatTag(Constants::SAM_RG_SAMPLE_TAG, rg.Sample); + // custom tags + if ( !rg.CustomTags.empty() ) { + for (size_t i = 0; i < rg.CustomTags.size(); ++i) { + const CustomHeaderTag& customTag = rg.CustomTags[i]; + out << FormatTag(customTag.TagName, customTag.TagValue); + } + } + // newline out << endl; } @@ -198,6 +221,14 @@ void SamFormatPrinter::PrintPG(std::stringstream& out) const { if ( pg.HasVersion() ) out << FormatTag(Constants::SAM_PG_VERSION_TAG, pg.Version); + // custom tags + if ( !pg.CustomTags.empty() ) { + for (size_t i = 0; i < pg.CustomTags.size(); ++i) { + const CustomHeaderTag& customTag = pg.CustomTags[i]; + out << FormatTag(customTag.TagName, customTag.TagValue); + } + } + // newline out << endl; } diff --git a/src/api/internal/sam/SamFormatPrinter_p.h b/src/api/internal/sam/SamFormatPrinter_p.h index ea29181..ec2e527 100644 --- a/src/api/internal/sam/SamFormatPrinter_p.h +++ b/src/api/internal/sam/SamFormatPrinter_p.h @@ -25,7 +25,7 @@ namespace BamTools { -class SamHeader; +struct SamHeader; namespace Internal { diff --git a/src/api/internal/sam/SamHeaderValidator_p.h b/src/api/internal/sam/SamHeaderValidator_p.h index 7d0c60a..aa7d8b4 100644 --- a/src/api/internal/sam/SamHeaderValidator_p.h +++ b/src/api/internal/sam/SamHeaderValidator_p.h @@ -26,9 +26,9 @@ namespace BamTools { -class SamHeader; -class SamReadGroup; -class SamSequence; +struct SamHeader; +struct SamReadGroup; +struct SamSequence; namespace Internal { diff --git a/src/toolkit/CMakeLists.txt b/src/toolkit/CMakeLists.txt index 33b0735..c781148 100644 --- a/src/toolkit/CMakeLists.txt +++ b/src/toolkit/CMakeLists.txt @@ -31,7 +31,7 @@ add_executable( bamtools_cmd # set BamTools application properties set_target_properties( bamtools_cmd PROPERTIES - VERSION 2.3.0 + VERSION 2.4.0 OUTPUT_NAME "bamtools" ) # make version info available in application diff --git a/src/toolkit/bamtools.cpp b/src/toolkit/bamtools.cpp index 29097d0..396b161 100644 --- a/src/toolkit/bamtools.cpp +++ b/src/toolkit/bamtools.cpp @@ -146,7 +146,7 @@ int Version(void) { int main(int argc, char* argv[]) { // just 'bamtools' - if ( (argc == 1) ) return Help(argc, argv); + if ( argc == 1 ) return Help(argc, argv); // 'bamtools help', 'bamtools --help', or 'bamtools -h' if ( IsHelp(argv[1]) ) return Help(argc, argv); diff --git a/src/toolkit/bamtools_filter.h b/src/toolkit/bamtools_filter.h index 7fa5f73..c82f420 100644 --- a/src/toolkit/bamtools_filter.h +++ b/src/toolkit/bamtools_filter.h @@ -28,7 +28,7 @@ class FilterTool : public AbstractTool { struct FilterSettings; FilterSettings* m_settings; - struct FilterToolPrivate; + class FilterToolPrivate; FilterToolPrivate* m_impl; }; diff --git a/src/toolkit/bamtools_resolve.cpp b/src/toolkit/bamtools_resolve.cpp index 9e5fb84..4c4d1a3 100644 --- a/src/toolkit/bamtools_resolve.cpp +++ b/src/toolkit/bamtools_resolve.cpp @@ -45,8 +45,6 @@ static const double DEFAULT_UNUSEDMODEL_THRESHOLD = 0.1; // basic char/string constants static const char COMMENT_CHAR = '#'; -static const char OPEN_BRACE_CHAR = '['; -static const char CLOSE_BRACE_CHAR = ']'; static const char EQUAL_CHAR = '='; static const char TAB_CHAR = '\t'; diff --git a/src/toolkit/bamtools_sort.h b/src/toolkit/bamtools_sort.h index d746f5e..a885fdd 100644 --- a/src/toolkit/bamtools_sort.h +++ b/src/toolkit/bamtools_sort.h @@ -28,7 +28,7 @@ class SortTool : public AbstractTool { struct SortSettings; SortSettings* m_settings; - struct SortToolPrivate; + class SortToolPrivate; SortToolPrivate* m_impl; }; diff --git a/src/toolkit/bamtools_split.h b/src/toolkit/bamtools_split.h index a294f4f..2c98dd5 100644 --- a/src/toolkit/bamtools_split.h +++ b/src/toolkit/bamtools_split.h @@ -29,7 +29,7 @@ class SplitTool : public AbstractTool { struct SplitSettings; SplitSettings* m_settings; - struct SplitToolPrivate; + class SplitToolPrivate; SplitToolPrivate* m_impl; }; diff --git a/src/utils/bamtools_fasta.cpp b/src/utils/bamtools_fasta.cpp index 680f62b..50f730a 100644 --- a/src/utils/bamtools_fasta.cpp +++ b/src/utils/bamtools_fasta.cpp @@ -77,7 +77,7 @@ void Fasta::FastaPrivate::Chomp(char* sequence) { static const int CHAR_LF = 10; static const int CHAR_CR = 13; - size_t seqLength = strlen(sequence); + int seqLength = strlen(sequence); if ( seqLength == 0 ) return; --seqLength; // ignore null terminator -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/bamtools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
