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clang-tidy --checks=readability-braces-around-statements
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@SoapZA
SoapZA committed May 30, 2021
1 parent 53e9c60 commit 9649a77
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Showing 58 changed files with 2,318 additions and 1,040 deletions.
135 changes: 91 additions & 44 deletions src/api/BamAlignment.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -109,7 +109,9 @@ bool BamAlignment::BuildCharData()
{

// skip if char data already parsed
if (!SupportData.HasCoreOnly) return true;
if (!SupportData.HasCoreOnly) {
return true;
}

// check system endianness
bool IsBigEndian = BamTools::SystemIsBigEndian();
Expand Down Expand Up @@ -149,14 +151,15 @@ bool BamAlignment::BuildCharData()
const char* qualData = SupportData.AllCharData.data() + qualDataOffset;

// if marked as unstored (sequence of 0xFF) - don't do conversion, just fill with 0xFFs
if (qualData[0] == (char)0xFF)
if (qualData[0] == (char)0xFF) {
Qualities.resize(SupportData.QuerySequenceLength, (char)0xFF);

// otherwise convert from numeric QV to 'FASTQ-style' ASCII character
else {
// otherwise convert from numeric QV to 'FASTQ-style' ASCII character
} else {
Qualities.reserve(SupportData.QuerySequenceLength);
for (std::size_t i = 0; i < SupportData.QuerySequenceLength; ++i)
for (std::size_t i = 0; i < SupportData.QuerySequenceLength; ++i) {
Qualities.append(1, qualData[i] + 33);
}
}
}

Expand Down Expand Up @@ -261,8 +264,9 @@ bool BamAlignment::BuildCharData()
case (Constants::BAM_TAG_TYPE_HEX):
case (Constants::BAM_TAG_TYPE_STRING):
// no endian swapping necessary for hex-string/string data
while (tagData[i])
while (tagData[i]) {
++i;
}
// increment one more for null terminator
++i;
break;
Expand Down Expand Up @@ -357,12 +361,20 @@ bool BamAlignment::FindTag(const std::string& tag, char*& pTagData,
numBytesParsed += 3;

// check the current tag, return true on match
if (std::strncmp(pTagType, tag.c_str(), 2) == 0) return true;
if (std::strncmp(pTagType, tag.c_str(), 2) == 0) {
return true;
}

// get the storage class and find the next tag
if (*pTagStorageType == '\0') return false;
if (!SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed)) return false;
if (*pTagData == '\0') return false;
if (*pTagStorageType == '\0') {
return false;
}
if (!SkipToNextTag(*pTagStorageType, pTagData, numBytesParsed)) {
return false;
}
if (*pTagData == '\0') {
return false;
}
}

// checked all tags, none match
Expand Down Expand Up @@ -475,7 +487,9 @@ int BamAlignment::GetEndPosition(bool usePadded, bool closedInterval) const

// increase end position on insertion, only if @usePadded is true
case Constants::BAM_CIGAR_INS_CHAR:
if (usePadded) alignEnd += op.Length;
if (usePadded) {
alignEnd += op.Length;
}
break;

// all other CIGAR chars do not affect end position
Expand All @@ -485,7 +499,9 @@ int BamAlignment::GetEndPosition(bool usePadded, bool closedInterval) const
}

// adjust for closedInterval, if requested
if (closedInterval) alignEnd -= 1;
if (closedInterval) {
alignEnd -= 1;
}

// return result
return alignEnd;
Expand Down Expand Up @@ -547,7 +563,9 @@ bool BamAlignment::GetSoftClips(std::vector<int>& clipSizes, std::vector<int>& r
// increase read position on insertion, genome position only if @usePadded is true
case Constants::BAM_CIGAR_INS_CHAR:
readPosition += op.Length;
if (usePadded) refPosition += op.Length;
if (usePadded) {
refPosition += op.Length;
}
break;

case Constants::BAM_CIGAR_SOFTCLIP_CHAR:
Expand All @@ -568,7 +586,9 @@ bool BamAlignment::GetSoftClips(std::vector<int>& clipSizes, std::vector<int>& r
//
// NOTE: This only needs to be done if the soft clip is the _first_ CIGAR op.
//////////////////////////////////////////////////////////////////////////////
if (firstCigarOp) readPosition += op.Length;
if (firstCigarOp) {
readPosition += op.Length;
}

// track the soft clip's size, read position, and genome position
clipSizes.push_back(op.Length);
Expand Down Expand Up @@ -602,7 +622,9 @@ std::vector<std::string> BamAlignment::GetTagNames() const
{

std::vector<std::string> result;
if (SupportData.HasCoreOnly || TagData.empty()) return result;
if (SupportData.HasCoreOnly || TagData.empty()) {
return result;
}

char* pTagData = (char*)TagData.data();
const unsigned int tagDataLength = TagData.size();
Expand All @@ -619,9 +641,15 @@ std::vector<std::string> BamAlignment::GetTagNames() const
result.push_back(std::string(pTagName, 2));

// find the next tag
if (*pTagType == '\0') break;
if (!SkipToNextTag(*pTagType, pTagData, numBytesParsed)) break;
if (*pTagData == '\0') break;
if (*pTagType == '\0') {
break;
}
if (!SkipToNextTag(*pTagType, pTagData, numBytesParsed)) {
break;
}
if (*pTagData == '\0') {
break;
}
}

return result;
Expand Down Expand Up @@ -696,7 +724,9 @@ bool BamAlignment::HasTag(const std::string& tag) const
{

// return false if no tag data present
if (SupportData.HasCoreOnly || TagData.empty()) return false;
if (SupportData.HasCoreOnly || TagData.empty()) {
return false;
}

// localize the tag data for lookup
char* pTagData = (char*)TagData.data();
Expand Down Expand Up @@ -827,10 +857,14 @@ void BamAlignment::RemoveTag(const std::string& tag)
{

// if char data not populated, do that first
if (SupportData.HasCoreOnly) BuildCharData();
if (SupportData.HasCoreOnly) {
BuildCharData();
}

// skip if no tags available
if (TagData.empty()) return;
if (TagData.empty()) {
return;
}

// localize the tag data
char* pOriginalTagData = (char*)TagData.data();
Expand All @@ -840,7 +874,9 @@ void BamAlignment::RemoveTag(const std::string& tag)
unsigned int numBytesParsed = 0;

// skip if tag not found
if (!FindTag(tag, pTagData, originalTagDataLength, numBytesParsed)) return;
if (!FindTag(tag, pTagData, originalTagDataLength, numBytesParsed)) {
return;
}

// otherwise, remove it
RaiiBuffer newTagData(originalTagDataLength);
Expand Down Expand Up @@ -888,120 +924,131 @@ void BamAlignment::SetErrorString(const std::string& where, const std::string& w
*/
void BamAlignment::SetIsDuplicate(bool ok)
{
if (ok)
if (ok) {
AlignmentFlag |= Constants::BAM_ALIGNMENT_DUPLICATE;
else
} else {
AlignmentFlag &= ~Constants::BAM_ALIGNMENT_DUPLICATE;
}
}

/*! \fn void BamAlignment::SetIsFailedQC(bool ok)
\brief Sets "failed quality control" flag to \a ok.
*/
void BamAlignment::SetIsFailedQC(bool ok)
{
if (ok)
if (ok) {
AlignmentFlag |= Constants::BAM_ALIGNMENT_QC_FAILED;
else
} else {
AlignmentFlag &= ~Constants::BAM_ALIGNMENT_QC_FAILED;
}
}

/*! \fn void BamAlignment::SetIsFirstMate(bool ok)
\brief Sets "alignment is first mate" flag to \a ok.
*/
void BamAlignment::SetIsFirstMate(bool ok)
{
if (ok)
if (ok) {
AlignmentFlag |= Constants::BAM_ALIGNMENT_READ_1;
else
} else {
AlignmentFlag &= ~Constants::BAM_ALIGNMENT_READ_1;
}
}

/*! \fn void BamAlignment::SetIsMapped(bool ok)
\brief Sets "alignment is mapped" flag to \a ok.
*/
void BamAlignment::SetIsMapped(bool ok)
{
if (ok)
if (ok) {
AlignmentFlag &= ~Constants::BAM_ALIGNMENT_UNMAPPED;
else
} else {
AlignmentFlag |= Constants::BAM_ALIGNMENT_UNMAPPED;
}
}

/*! \fn void BamAlignment::SetIsMateMapped(bool ok)
\brief Sets "alignment's mate is mapped" flag to \a ok.
*/
void BamAlignment::SetIsMateMapped(bool ok)
{
if (ok)
if (ok) {
AlignmentFlag &= ~Constants::BAM_ALIGNMENT_MATE_UNMAPPED;
else
} else {
AlignmentFlag |= Constants::BAM_ALIGNMENT_MATE_UNMAPPED;
}
}

/*! \fn void BamAlignment::SetIsMateReverseStrand(bool ok)
\brief Sets "alignment's mate mapped to reverse strand" flag to \a ok.
*/
void BamAlignment::SetIsMateReverseStrand(bool ok)
{
if (ok)
if (ok) {
AlignmentFlag |= Constants::BAM_ALIGNMENT_MATE_REVERSE_STRAND;
else
} else {
AlignmentFlag &= ~Constants::BAM_ALIGNMENT_MATE_REVERSE_STRAND;
}
}

/*! \fn void BamAlignment::SetIsPaired(bool ok)
\brief Sets "alignment part of paired-end read" flag to \a ok.
*/
void BamAlignment::SetIsPaired(bool ok)
{
if (ok)
if (ok) {
AlignmentFlag |= Constants::BAM_ALIGNMENT_PAIRED;
else
} else {
AlignmentFlag &= ~Constants::BAM_ALIGNMENT_PAIRED;
}
}

/*! \fn void BamAlignment::SetIsPrimaryAlignment(bool ok)
\brief Sets "position is primary alignment" flag to \a ok.
*/
void BamAlignment::SetIsPrimaryAlignment(bool ok)
{
if (ok)
if (ok) {
AlignmentFlag &= ~Constants::BAM_ALIGNMENT_SECONDARY;
else
} else {
AlignmentFlag |= Constants::BAM_ALIGNMENT_SECONDARY;
}
}

/*! \fn void BamAlignment::SetIsProperPair(bool ok)
\brief Sets "alignment is part of read that satisfied paired-end resolution" flag to \a ok.
*/
void BamAlignment::SetIsProperPair(bool ok)
{
if (ok)
if (ok) {
AlignmentFlag |= Constants::BAM_ALIGNMENT_PROPER_PAIR;
else
} else {
AlignmentFlag &= ~Constants::BAM_ALIGNMENT_PROPER_PAIR;
}
}

/*! \fn void BamAlignment::SetIsReverseStrand(bool ok)
\brief Sets "alignment mapped to reverse strand" flag to \a ok.
*/
void BamAlignment::SetIsReverseStrand(bool ok)
{
if (ok)
if (ok) {
AlignmentFlag |= Constants::BAM_ALIGNMENT_REVERSE_STRAND;
else
} else {
AlignmentFlag &= ~Constants::BAM_ALIGNMENT_REVERSE_STRAND;
}
}

/*! \fn void BamAlignment::SetIsSecondMate(bool ok)
\brief Sets "alignment is second mate on read" flag to \a ok.
*/
void BamAlignment::SetIsSecondMate(bool ok)
{
if (ok)
if (ok) {
AlignmentFlag |= Constants::BAM_ALIGNMENT_READ_2;
else
} else {
AlignmentFlag &= ~Constants::BAM_ALIGNMENT_READ_2;
}
}

/*! \fn bool BamAlignment::SkipToNextTag(const char storageType, char*& pTagData, unsigned int& numBytesParsed) const
Expand Down
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