+++ /dev/null
-// ***************************************************************************
-// SamFormatParser.cpp (c) 2010 Derek Barnett
-// Marth Lab, Department of Biology, Boston College
-// ---------------------------------------------------------------------------
-// Last modified: 10 October 2011 (DB)
-// ---------------------------------------------------------------------------
-// Provides functionality for parsing SAM header text into SamHeader object
-// ***************************************************************************
-
-#include "api/SamConstants.h"
-#include "api/SamHeader.h"
-#include "api/internal/BamException_p.h"
-#include "api/internal/SamFormatParser_p.h"
-using namespace BamTools;
-using namespace BamTools::Internal;
-
-#include <iostream>
-#include <sstream>
-#include <vector>
-using namespace std;
-
-SamFormatParser::SamFormatParser(SamHeader& header)
- : m_header(header)
-{ }
-
-SamFormatParser::~SamFormatParser(void) { }
-
-void SamFormatParser::Parse(const string& headerText) {
-
- // clear header's prior contents
- m_header.Clear();
-
- // empty header is OK, but skip processing
- if ( headerText.empty() )
- return;
-
- // other wise parse SAM lines
- istringstream headerStream(headerText);
- string headerLine("");
- while ( getline(headerStream, headerLine) )
- ParseSamLine(headerLine);
-}
-
-void SamFormatParser::ParseSamLine(const string& line) {
-
- // skip if line is not long enough to contain true values
- if ( line.length() < 5 ) return;
-
- // determine token at beginning of line
- const string firstToken = line.substr(0,3);
- string restOfLine = line.substr(4);
- if ( firstToken == Constants::SAM_HD_BEGIN_TOKEN) ParseHDLine(restOfLine);
- else if ( firstToken == Constants::SAM_SQ_BEGIN_TOKEN) ParseSQLine(restOfLine);
- else if ( firstToken == Constants::SAM_RG_BEGIN_TOKEN) ParseRGLine(restOfLine);
- else if ( firstToken == Constants::SAM_PG_BEGIN_TOKEN) ParsePGLine(restOfLine);
- else if ( firstToken == Constants::SAM_CO_BEGIN_TOKEN) ParseCOLine(restOfLine);
- else {
- const string message = string("unknown token: ") + firstToken;
- throw BamException("SamFormatParser::ParseSamLine", message);
- }
-}
-
-void SamFormatParser::ParseHDLine(const string& line) {
-
- // split HD lines into tokens
- vector<string> tokens = Split(line, Constants::SAM_TAB);
-
- // iterate over tokens
- 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 {
- const string message = string("unknown HD tag: ") + tokenTag;
- throw BamException("SamFormatParser::ParseHDLine", message);
- }
- }
-
- // check for required tags
- if ( !m_header.HasVersion() )
- throw BamException("SamFormatParser::ParseHDLine", "@HD line is missing VN tag");
-}
-
-void SamFormatParser::ParseSQLine(const string& line) {
-
- SamSequence seq;
-
- // split SQ line into tokens
- vector<string> tokens = Split(line, Constants::SAM_TAB);
-
- // iterate over tokens
- 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 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 {
- const string message = string("unknown SQ tag: ") + tokenTag;
- throw BamException("SamFormatParser::ParseSQLine", message);
- }
- }
-
- // check for required tags
- if ( !seq.HasName() )
- throw BamException("SamFormatParser::ParseSQLine", "@SQ line is missing SN tag");
- if ( !seq.HasLength() )
- throw BamException("SamFormatParser::ParseSQLine", "@SQ line is missing LN tag");
-
- // store SAM sequence entry
- m_header.Sequences.Add(seq);
-}
-
-void SamFormatParser::ParseRGLine(const string& line) {
-
- SamReadGroup rg;
-
- // split string into tokens
- vector<string> tokens = Split(line, Constants::SAM_TAB);
-
- // iterate over tokens
- vector<string>::const_iterator tokenIter = tokens.begin();
- vector<string>::const_iterator tokenEnd = tokens.end();
- for ( ; tokenIter != tokenEnd; ++tokenIter ) {
-
- // 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 {
- const string message = string("unknown RG tag: ") + tokenTag;
- throw BamException("SamFormatParser::ParseRGLine", message);
- }
- }
-
- // check for required tags
- if ( !rg.HasID() )
- throw BamException("SamFormatParser::ParseRGLine", "@RG line is missing ID tag");
-
- // store SAM read group entry
- 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);
-
- // iterate over tokens
- vector<string>::const_iterator tokenIter = tokens.begin();
- vector<string>::const_iterator tokenEnd = tokens.end();
- for ( ; tokenIter != tokenEnd; ++tokenIter ) {
-
- // 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 {
- const string message = string("unknown PG tag: ") + tokenTag;
- throw BamException("SamFormatParser::ParsePGLine", message);
- }
- }
-
- // check for required tags
- if ( !pg.HasID() )
- throw BamException("SamFormatParser::ParsePGLine", "@PG line is missing ID tag");
-
- // store SAM program entry
- m_header.Programs.Add(pg);
-}
-
-void SamFormatParser::ParseCOLine(const string& line) {
- // simply add line to comments list
- m_header.Comments.push_back(line);
-}
-
-const vector<string> SamFormatParser::Split(const string& line, const char delim) {
- vector<string> tokens;
- stringstream lineStream(line);
- string token;
- while ( getline(lineStream, token, delim) )
- tokens.push_back(token);
- return tokens;
-}
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