// Marth Lab, Department of Biology, Boston College
// All rights reserved.
// ---------------------------------------------------------------------------
-// Last modified: 23 December 2010 (DB)
+// Last modified: 19 April 2011 (DB)
// ---------------------------------------------------------------------------
// Provides functionality for parsing SAM header text into SamHeader object
// ***************************************************************************
string headerLine("");
while ( getline(headerStream, headerLine) )
ParseSamLine(headerLine);
- return;
}
void SamFormatParser::ParseSamLine(const string& line) {
else if ( firstToken == Constants::SAM_CO_BEGIN_TOKEN) ParseCOLine(restOfLine);
else
cerr << "SamFormatParser ERROR: unknown token: " << firstToken << endl;
-
- return;
}
void SamFormatParser::ParseHDLine(const string& line) {
// set header contents
if ( tokenTag == Constants::SAM_HD_VERSION_TAG ) m_header.Version = tokenValue;
- else if ( tokenTag == Constants::SAM_HD_GROUPORDER_TAG ) m_header.GroupOrder = 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
cerr << "SamFormatParser ERROR: unknown HD tag: " << tokenTag << endl;
}
// if @HD line exists, VN must be provided
- if ( !m_header.HasVersion() ) {
+ if ( !m_header.HasVersion() )
cerr << "SamFormatParser ERROR: @HD line is missing VN tag" << endl;
- return;
- }
}
void SamFormatParser::ParseSQLine(const string& line) {
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_URI_TAG ) seq.URI = 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
cerr << "SamFormatParser ERROR: unknown SQ tag: " << tokenTag << endl;
}
+ bool isMissingRequiredFields = false;
+
// if @SQ line exists, SN must be provided
if ( !seq.HasName() ) {
+ isMissingRequiredFields = true;
cerr << "SamFormatParser ERROR: @SQ line is missing SN tag" << endl;
- return;
}
// if @SQ line exists, LN must be provided
if ( !seq.HasLength() ) {
+ isMissingRequiredFields = true;
cerr << "SamFormatParser ERROR: @SQ line is missing LN tag" << endl;
- return;
}
// store SAM sequence entry
- m_header.Sequences.Add(seq);
+ if ( !isMissingRequiredFields )
+ m_header.Sequences.Add(seq);
}
void SamFormatParser::ParseRGLine(const string& line) {
// set read group contents
if ( tokenTag == Constants::SAM_RG_ID_TAG ) rg.ID = tokenValue;
- else if ( tokenTag == Constants::SAM_RG_SAMPLE_TAG ) rg.Sample = tokenValue;
- else if ( tokenTag == Constants::SAM_RG_LIBRARY_TAG ) rg.Library = 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_SEQCENTER_TAG ) rg.SequencingCenter = 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
cerr << "SamFormatParser ERROR: unknown RG tag: " << tokenTag << endl;
}
+ bool isMissingRequiredFields = false;
+
// if @RG line exists, ID must be provided
if ( !rg.HasID() ) {
+ isMissingRequiredFields = true;
cerr << "SamFormatParser ERROR: @RG line is missing ID tag" << endl;
- return;
- }
-
- // if @RG line exists, SM must be provided
- if ( !rg.HasSample() ) {
- cerr << "SamFormatParser ERROR: @RG line is missing SM tag" << endl;
- return;
}
// store SAM read group entry
- m_header.ReadGroups.Add(rg);
+ if ( !isMissingRequiredFields )
+ m_header.ReadGroups.Add(rg);
}
void SamFormatParser::ParsePGLine(const string& line) {
+ SamProgram pg;
+
// split string into tokens
vector<string> tokens = Split(line, Constants::SAM_TAB);
const string tokenTag = (*tokenIter).substr(0,2);
const string tokenValue = (*tokenIter).substr(3);
- // set header contents
- if ( tokenTag == Constants::SAM_PG_NAME_TAG ) m_header.ProgramName = tokenValue;
- else if ( tokenTag == Constants::SAM_PG_VERSION_TAG ) m_header.ProgramVersion = tokenValue;
- else if ( tokenTag == Constants::SAM_PG_COMMANDLINE_TAG ) m_header.ProgramCommandLine = tokenValue;
+ // 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
cerr << "SamFormatParser ERROR: unknown PG tag: " << tokenTag << endl;
}
+ bool isMissingRequiredFields = false;
+
// if @PG line exists, ID must be provided
- if ( !m_header.HasProgramName() ) {
- cerr << "SamFormatParser ERROR:- @PG line is missing ID tag" << endl;
- return;
+ if ( !pg.HasID() ) {
+ isMissingRequiredFields = true;
+ cerr << "SamFormatParser ERROR: @PG line is missing ID tag" << endl;
}
+
+ // store SAM program record
+ if ( !isMissingRequiredFields )
+ m_header.Programs.Add(pg);
}
void SamFormatParser::ParseCOLine(const string& line) {