114 lines
3.1 KiB
C
114 lines
3.1 KiB
C
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/*
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* Copyright 2020, Yun (Leo) Zhang <imzhangyun@gmail.com>
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*
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* This file is part of HISAT-3N.
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*
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* HISAT-3N is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* HISAT-3N is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with HISAT-3N. If not, see <http://www.gnu.org/licenses/>.
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*/
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#ifndef HISAT2_UTILITY_3N_H
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#define HISAT2_UTILITY_3N_H
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#include <string>
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using namespace std;
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/**
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* this is the class to convert asc2dna, asc2dnacomp, and dnacomp matrix for hisat-3n conversion.
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* always save the conversion as convertFrom and convertTo.
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* this class is to convert matrix for hisat2-build with (--3N) or hisat2-repeat with (--3N).
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* hisat2 with (--base-change C,T) will not use this class.
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*/
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class ConvertMatrix3N {
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char convertFrom = 'A';
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char convertTo = 'A';
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string allBase = "ACGT";
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string allBaseLower = "acgt";
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/**
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* helper function to convert character to int presentation.
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*/
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int charToInt(char inputChar) { return allBase.find(inputChar); }
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/**
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* return the complement nucleotide
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*/
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int complement(char inputChar) { return allBase[3-charToInt(inputChar)]; }
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/**
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* convert asc2dna, asc2dnacomp, and dnacomp matrix according to convertFrom and convertTo variable.
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* always restore the matrix to original (4 letter) matrix.
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*/
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void convertMatrix() ;
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public:
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ConvertMatrix3N(){
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};
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/**
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* save the conversion information then convert the matrix.
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*/
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void convert(char from, char to) {
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convertFrom = from;
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convertTo = to;
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convertMatrix();
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}
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/**
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* change convertFrom and convertTO to it's complement nucleotide, then convert the matrix.
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*/
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void inverseConversion() {
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convertFrom = complement(convertFrom);
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convertTo = complement(convertTo);
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convertMatrix();
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}
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/**
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* restore the asc2dna, asc2dnacomp, and dnacomp matrix to original (4 letter).
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* do not change the convertFrom and convertTO variable.
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*/
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void restoreNormal() ;
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/**
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* convert the matrix according to the convertFrom and convertTo variable.
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*/
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void restoreConversion() {
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convertMatrix();
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}
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};
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/**
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* the simple data structure to store cigar information.
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*/
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class Cigar {
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int len;
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char label;
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public:
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Cigar() { }
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Cigar(int inputLen, char inputLabel): len(inputLen), label(inputLabel) {
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}
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int& getLen() { return len; }
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char& getLabel() { return label; }
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};
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extern void getConversion(char usrInputFrom, char usrInputTo, char& convertFrom, char& convertTo);
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extern bool fileExist (string name);
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#endif //HISAT2_UTILITY_3N_H
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