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Fix clang 17 #232

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merged 2 commits into from
Dec 15, 2023
Merged

Fix clang 17 #232

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5028748
Fix `-Wunused-but-set-variable`
SoapZA Dec 15, 2023
62be9f5
Remove deprecated `std::binary_function`
SoapZA Dec 15, 2023
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2 changes: 0 additions & 2 deletions src/api/BamAlignment.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -870,7 +870,6 @@ void BamAlignment::RemoveTag(const std::string& tag)
char* pOriginalTagData = (char*)TagData.data();
char* pTagData = pOriginalTagData;
const unsigned int originalTagDataLength = TagData.size();
unsigned int newTagDataLength = 0;
unsigned int numBytesParsed = 0;

// skip if tag not found
Expand All @@ -885,7 +884,6 @@ void BamAlignment::RemoveTag(const std::string& tag)
pTagData -= 3;
numBytesParsed -= 3;
const unsigned int beginningTagDataLength = numBytesParsed;
newTagDataLength += beginningTagDataLength;
std::memcpy(newTagData.Buffer, pOriginalTagData, numBytesParsed);

// attemp to skip to next tag
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11 changes: 4 additions & 7 deletions src/api/algorithms/Sort.h
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Expand Up @@ -60,9 +60,6 @@ struct API_EXPORT Sort
return false; // <-- unreachable
}

//! Base class for our sorting function objects
typedef std::binary_function<BamAlignment, BamAlignment, bool> AlignmentSortBase;

/*! \struct BamTools::Algorithms::Sort::ByName
\brief Function object for comparing alignments by name

Expand All @@ -79,7 +76,7 @@ struct API_EXPORT Sort
std::sort( a.begin(), a.end(), Sort::ByName(Sort::DescendingOrder) );
\endcode
*/
struct ByName : public AlignmentSortBase
struct ByName
{

// ctor
Expand Down Expand Up @@ -120,7 +117,7 @@ struct API_EXPORT Sort
std::sort( a.begin(), a.end(), Sort::ByPosition(Sort::DescendingOrder) );
\endcode
*/
struct ByPosition : public AlignmentSortBase
struct ByPosition
{

// ctor
Expand Down Expand Up @@ -177,7 +174,7 @@ struct API_EXPORT Sort
\endcode
*/
template <typename T>
struct ByTag : public AlignmentSortBase
struct ByTag
{

// ctor
Expand Down Expand Up @@ -227,7 +224,7 @@ struct API_EXPORT Sort
std::set<BamAlignment, Sort::Unsorted>; // STL set, unsorted (but probably insertion order)
\endcode
*/
struct Unsorted : public AlignmentSortBase
struct Unsorted
{

// comparison function
Expand Down
2 changes: 1 addition & 1 deletion src/api/internal/bam/BamMultiMerger_p.h
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Expand Up @@ -49,7 +49,7 @@ struct API_NO_EXPORT MergeItem
};

template <typename Compare>
struct API_NO_EXPORT MergeItemSorter : public std::binary_function<MergeItem, MergeItem, bool>
struct API_NO_EXPORT MergeItemSorter
{

public:
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4 changes: 0 additions & 4 deletions src/utils/bamtools_fasta.cpp
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Expand Up @@ -175,7 +175,6 @@ bool Fasta::FastaPrivate::CreateIndex(const std::string& indexFilename)
}

// iterate through fasta entries
int currentId = 0;
std::string header;
std::string sequence;
while (GetNextHeader(header)) {
Expand Down Expand Up @@ -207,9 +206,6 @@ bool Fasta::FastaPrivate::CreateIndex(const std::string& indexFilename)

// store index entry
Index.push_back(data);

// update ref Id
++currentId;
}

// open index file
Expand Down