[med-svn] [bamtools] 01/05: Imported Upstream version 2.4.0+dfsg
Kevin Murray
daube-guest at moszumanska.debian.org
Thu Sep 24 07:41:22 UTC 2015
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a commit to branch master
in repository bamtools.
commit 00cf2a2de2070b110c6d464c6b216066839966f3
Author: Kevin Murray <spam at kdmurray.id.au>
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
--
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