/usr/include/blasr/format/StickAlignmentPrinter.hpp is in libblasr-dev 0~20151014+gitbe5d1bf-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 | #ifndef _BLASR_STICK_ALIGNMENT_PRINTER_HPP_
#define _BLASR_STICK_ALIGNMENT_PRINTER_HPP_
#include <string>
#include <iostream>
#include <fstream>
#include "datastructures/alignment/Alignment.hpp"
#include "algorithms/alignment/AlignmentUtils.hpp"
template<typename T_Alignment, typename T_QuerySequence, typename T_TargetSequence>
void StickPrintAlignment(T_Alignment &alignment,
T_QuerySequence &query, T_TargetSequence &text, std::ostream &out,
unsigned int qPrintStart = 0,
unsigned int tPrintStart = 0,
int maxPrintLength = 50) {
//
// Eventually hack to add options for alignment format.
//
std::string queryStr, alignStr, textStr;
char gapChar = '-';
//
// [q/t]PrintStart are the beginning/ending of the subsequence that
// is being printed however the actual alignment begins at
// [q/t]PrintStart + alignment->[q/t]Pos, since there may be a small
// gap between the beginning of the alignment and the beginning of
// the substring that is aligned.
//
out << " Query: " << alignment.qName << endl;
out << " Target: " << alignment.tName << endl;
out << " Model: a hybrid of global/local non-affine alignment" <<endl;
out << " Raw score: " << alignment.score << endl;
out << " Map QV: " << alignment.mapQV << endl;
out << " Query strand: " << alignment.qStrand << endl;
out << " Target strand: " << alignment.tStrand << endl;
if (alignment.blocks.size() > 0) {
out << " QueryRange: " << qPrintStart + alignment.qPos //alignment.blocks[0].qPos
<< " -> "
<< (qPrintStart + alignment.qPos +
+ alignment.blocks[alignment.blocks.size() - 1 ].qPos
+ alignment.blocks[alignment.blocks.size() - 1 ].length) << " of " << alignment.qLength << endl;
out << " TargetRange: " << tPrintStart + alignment.tPos //alignment.blocks[0].tPos
<< " -> "
// << (tPrintStart + alignment.blocks[alignment.blocks.size() - 1].tPos +
<< (tPrintStart + alignment.tPos +
alignment.blocks[alignment.blocks.size() - 1 ].tPos +
alignment.blocks[alignment.blocks.size() - 1].length) << " of " << alignment.tLength << endl;
}
else {
out << " QueryRange: NONE " << endl;
out << " TargetRange: NONE " << endl;
}
if (alignment.blocks.size() == 0)
return;
CreateAlignmentStrings(alignment, query.seq, text.seq, textStr, alignStr, queryStr, query.length, text.length);
//
// Process any gaps at the beginning of
// the alignment.
//
DNALength qPos, tPos;
int coordsPrintWidth = MAX(GetNumberWidth(alignment.qPos + qPrintStart + query.length),
GetNumberWidth(alignment.tPos + tPrintStart + query.length));
//
// Now print the alignment
VectorIndex lineLength = maxPrintLength;
if (lineLength > textStr.size())
lineLength = textStr.size();
std::string textLine, queryLine, alignLine;
DNALength pos = 0;
tPos = alignment.tPos;
qPos = alignment.qPos;
int spacePad = 2;
std::string coordPadding(spacePad, ' ');
std::string alignStrPadding(coordsPrintWidth + spacePad, ' ');
while (lineLength > 0) {
textLine.assign(textStr, pos, lineLength);
alignLine.assign(alignStr, pos, lineLength);
queryLine.assign(queryStr, pos, lineLength);
out.width(coordsPrintWidth);
out << qPrintStart + qPos;
out.width(0);
out << coordPadding << queryLine << endl;
out << alignStrPadding << alignLine << endl;
out.width(coordsPrintWidth);
out << tPrintStart + tPos ;
out.width(0);
out << coordPadding << textLine << endl;
out << endl;
pos += lineLength;
tPos += lineLength;
qPos += lineLength;
//
// Adjust tPos and qPos for indels.
//
VectorIndex p;
for (p = 0; p < textLine.size(); p++) {
if (textLine[p] == gapChar)
tPos--;
}
for (p = 0; p < queryLine.size(); p++) {
if (queryLine[p] == gapChar)
qPos--;
}
lineLength = maxPrintLength;
if (textStr.size() < (pos +lineLength)) {
// sets lineLength to 0 on the last iteration
lineLength = textStr.size() - pos;
}
else {
lineLength = maxPrintLength;
}
}
}
#endif // _BLASR_STICK_ALIGNMENT_PRINTER_HPP_
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