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#ifndef _BLASR_XML_PRINTER_HPP_
#define _BLASR_XML_PRINTER_HPP_
#include <alignment/utils/SimpleXMLUtils.hpp>
namespace XMLOutput {
template <typename T_Alignment, typename T_Sequence>
void Print(T_Alignment &alignment, T_Sequence &query, T_Sequence &text, std::ostream &out,
int qPrintStart = 0, int tPrintStart = 0, int maxPrintLength = 50)
{
(void)(qPrintStart);
(void)(tPrintStart);
(void)(maxPrintLength);
/*
* Sample alignment:
*
<hit name="x15_y33_1220208-0008_m081205_152444_Uni_p2_b15" unalignedLength="1301" start="1051" end="1016" strand="-" targetStart="1" targetEnd="44" targetStrand="+">
<zScore value="-6.091"/>
<nInsert value="1" percent="2.86" />
<nDelete value="9" percent="25.71" />
<nMismatch value="1" percent="2.86" />
<nCorrect value="24" percent="68.57" />
<alignment><query>
AG--CGTTCC-TATGG-TG-GGGTCGTTA-ACT---GTCGCCAG
</query><target>
AGCCCG-TCCTTATGGTTGAGGGTTGTTACACTTCGGTCGCCAG
</target></alignment>
</hit>
*/
char strand[2] = {'+', '-'};
std::string tAlignStr, alignStr, qAlignStr;
CreateAlignmentStrings(alignment, query.seq, text.seq, tAlignStr, alignStr, qAlignStr);
int alignLength = tAlignStr.size();
if (alignLength == 0) {
alignLength = 1; // Make sure there are no divide by zero.
alignment.nIns = 0;
alignment.nDel = 0;
alignment.nMismatch = 0;
alignment.nMatch = 0;
}
out << BeginDataEntry(
std::string("hit"),
CreateKeywordValuePair(std::string("name"), alignment.qName) +
CreateKeywordValuePair(std::string("unalignedLength"), alignment.qLength) +
CreateKeywordValuePair(std::string("start"), alignment.qPos) +
CreateKeywordValuePair(std::string("end"),
alignment.qPos + alignment.qAlignLength) +
CreateKeywordValuePair(std::string("strand"), strand[alignment.qStrand]) +
CreateKeywordValuePair(std::string("targetStart"), alignment.tPos) +
CreateKeywordValuePair(std::string("targetEnd"),
alignment.tPos + alignment.tAlignLength) +
CreateKeywordValuePair(std::string("targetStrand"), strand[alignment.tStrand]))
<< std::endl;
out << CreateDataEntry(std::string("zScore"),
CreateKeywordValuePair(std::string("value"), alignment.zScore))
<< std::endl;
out << CreateDataEntry(std::string("nInsert"),
CreateKeywordValuePair(std::string("value"), alignment.nIns) + " " +
CreateKeywordValuePair(std::string("percent"),
alignment.nIns * 0.5 / alignLength))
<< std::endl;
out << CreateDataEntry(std::string("nDelete"),
CreateKeywordValuePair(std::string("value"), alignment.nDel) + " " +
CreateKeywordValuePair(std::string("percent"),
alignment.nDel * 0.5 / alignLength))
<< std::endl;
out << CreateDataEntry(std::string("nMismatch"),
CreateKeywordValuePair(std::string("value"), alignment.nMismatch) + " " +
CreateKeywordValuePair(std::string("percent"),
alignment.nMismatch * 0.5 / alignLength))
<< std::endl;
out << CreateDataEntry(std::string("nCorrect"),
CreateKeywordValuePair(std::string("value"), alignment.nMatch) + " " +
CreateKeywordValuePair(std::string("percent"),
alignment.nMatch * 0.5 / alignLength))
<< std::endl;
out << CreateStartEntry(std::string("alignment"), std::string(""))
<< CreateStartEntry(std::string("query"), std::string("")) << std::endl;
out << qAlignStr << std::endl;
out << CreateEndEntry(std::string("query")) << std::endl;
out << CreateStartEntry(std::string("target"), std::string("")) << std::endl;
out << tAlignStr << std::endl;
out << CreateEndEntry(std::string("target")) << std::endl;
out << CreateEndEntry(std::string("alignment")) << std::endl;
out << CreateEndEntry(std::string("hit")) << std::endl;
}
}
#endif
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