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Checking if the input string while parsing the SAM header is not empty #143

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138 changes: 71 additions & 67 deletions src/api/internal/sam/SamFormatParser_p.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -65,20 +65,21 @@ void SamFormatParser::ParseHDLine(const string& line) {
vector<string>::const_iterator tokenIter = tokens.begin();
vector<string>::const_iterator tokenEnd = tokens.end();
for ( ; tokenIter != tokenEnd; ++tokenIter ) {

// get tag/value
const string tokenTag = (*tokenIter).substr(0,2);
const string tokenValue = (*tokenIter).substr(3);

// set header contents
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);
if (!(*tokenIter).empty()){
// get tag/value
const string tokenTag = (*tokenIter).substr(0, 2);
const string tokenValue = (*tokenIter).substr(3);

// set header contents
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);
}
}
}

Expand All @@ -98,23 +99,24 @@ void SamFormatParser::ParseSQLine(const string& line) {
vector<string>::const_iterator tokenIter = tokens.begin();
vector<string>::const_iterator tokenEnd = tokens.end();
for ( ; tokenIter != tokenEnd; ++tokenIter ) {

if (!(*tokenIter).empty()){
// get tag/value
const string tokenTag = (*tokenIter).substr(0,2);
const string tokenValue = (*tokenIter).substr(3);

// set sequence contents
if ( tokenTag == Constants::SAM_SQ_NAME_TAG ) seq.Name = tokenValue;
else if ( tokenTag == Constants::SAM_SQ_LENGTH_TAG ) seq.Length = tokenValue;
else if ( tokenTag == Constants::SAM_SQ_ASSEMBLYID_TAG ) seq.AssemblyID = tokenValue;
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);
const string tokenTag = (*tokenIter).substr(0, 2);
const string tokenValue = (*tokenIter).substr(3);

// set sequence contents
if (tokenTag == Constants::SAM_SQ_NAME_TAG) seq.Name = tokenValue;
else if (tokenTag == Constants::SAM_SQ_LENGTH_TAG) seq.Length = tokenValue;
else if (tokenTag == Constants::SAM_SQ_ASSEMBLYID_TAG) seq.AssemblyID = tokenValue;
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);
}
}
}

Expand All @@ -139,29 +141,30 @@ void SamFormatParser::ParseRGLine(const string& line) {
vector<string>::const_iterator tokenIter = tokens.begin();
vector<string>::const_iterator tokenEnd = tokens.end();
for ( ; tokenIter != tokenEnd; ++tokenIter ) {

if (!(*tokenIter).empty()){
// get token tag/value
const string tokenTag = (*tokenIter).substr(0,2);
const string tokenValue = (*tokenIter).substr(3);

// set read group contents
if ( tokenTag == Constants::SAM_RG_ID_TAG ) rg.ID = tokenValue;
else if ( tokenTag == Constants::SAM_RG_DESCRIPTION_TAG ) rg.Description = tokenValue;
else if ( tokenTag == Constants::SAM_RG_FLOWORDER_TAG ) rg.FlowOrder = tokenValue;
else if ( tokenTag == Constants::SAM_RG_KEYSEQUENCE_TAG ) rg.KeySequence = tokenValue;
else if ( tokenTag == Constants::SAM_RG_LIBRARY_TAG ) rg.Library = tokenValue;
else if ( tokenTag == Constants::SAM_RG_PLATFORMUNIT_TAG ) rg.PlatformUnit = tokenValue;
else if ( tokenTag == Constants::SAM_RG_PREDICTEDINSERTSIZE_TAG ) rg.PredictedInsertSize = tokenValue;
else if ( tokenTag == Constants::SAM_RG_PRODUCTIONDATE_TAG ) rg.ProductionDate = tokenValue;
else if ( tokenTag == Constants::SAM_RG_PROGRAM_TAG ) rg.Program = tokenValue;
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);
const string tokenTag = (*tokenIter).substr(0, 2);
const string tokenValue = (*tokenIter).substr(3);

// set read group contents
if (tokenTag == Constants::SAM_RG_ID_TAG) rg.ID = tokenValue;
else if (tokenTag == Constants::SAM_RG_DESCRIPTION_TAG) rg.Description = tokenValue;
else if (tokenTag == Constants::SAM_RG_FLOWORDER_TAG) rg.FlowOrder = tokenValue;
else if (tokenTag == Constants::SAM_RG_KEYSEQUENCE_TAG) rg.KeySequence = tokenValue;
else if (tokenTag == Constants::SAM_RG_LIBRARY_TAG) rg.Library = tokenValue;
else if (tokenTag == Constants::SAM_RG_PLATFORMUNIT_TAG) rg.PlatformUnit = tokenValue;
else if (tokenTag == Constants::SAM_RG_PREDICTEDINSERTSIZE_TAG) rg.PredictedInsertSize = tokenValue;
else if (tokenTag == Constants::SAM_RG_PRODUCTIONDATE_TAG) rg.ProductionDate = tokenValue;
else if (tokenTag == Constants::SAM_RG_PROGRAM_TAG) rg.Program = tokenValue;
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);
}
}
}

Expand All @@ -184,22 +187,23 @@ void SamFormatParser::ParsePGLine(const string& line) {
vector<string>::const_iterator tokenIter = tokens.begin();
vector<string>::const_iterator tokenEnd = tokens.end();
for ( ; tokenIter != tokenEnd; ++tokenIter ) {

if (!(*tokenIter).empty()){
// get token tag/value
const string tokenTag = (*tokenIter).substr(0,2);
const string tokenValue = (*tokenIter).substr(3);

// set program record contents
if ( tokenTag == Constants::SAM_PG_ID_TAG ) pg.ID = tokenValue;
else if ( tokenTag == Constants::SAM_PG_NAME_TAG ) pg.Name = tokenValue;
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);
const string tokenTag = (*tokenIter).substr(0, 2);
const string tokenValue = (*tokenIter).substr(3);

// set program record contents
if (tokenTag == Constants::SAM_PG_ID_TAG) pg.ID = tokenValue;
else if (tokenTag == Constants::SAM_PG_NAME_TAG) pg.Name = tokenValue;
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);
}
}
}

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