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/*
* Copyright 2015, Daehwan Kim <infphilo@gmail.com>
*
* This file is part of HISAT 2.
*
* HISAT 2 is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* HISAT 2 is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with HISAT 2. If not, see <http://www.gnu.org/licenses/>.
*/
/*
* tp.h
*
*/
#ifndef TP_H_
#define TP_H_
#include <iostream>
#include <stdint.h>
/**
* Encapsulates alignment policy for transcriptome
*/
class TranscriptomePolicy {
public:
TranscriptomePolicy() { reset(); }
TranscriptomePolicy(
size_t minIntronLen,
size_t maxIntronLen,
uint32_t minAnchorLen = 7,
uint32_t minAnchorLen_noncan = 14,
bool no_spliced_alignment = false,
bool transcriptome_mapping_only = false,
bool transcriptome_assembly = false,
bool xs_only = false,
bool avoid_pseudogene = false)
{
init(minIntronLen,
maxIntronLen,
minAnchorLen,
minAnchorLen_noncan,
no_spliced_alignment,
transcriptome_mapping_only,
transcriptome_assembly,
xs_only,
avoid_pseudogene);
}
/**
*/
void reset() {
init(false, false, false);
}
/**
*/
void init(
size_t minIntronLen,
size_t maxIntronLen,
uint32_t minAnchorLen = 7,
uint32_t minAnchorLen_noncan = 14,
bool no_spliced_alignment = false,
bool transcriptome_mapping_only = false,
bool transcriptome_assembly = false,
bool xs_only = false,
bool avoid_pseudogene = false)
{
minIntronLen_ = minIntronLen;
maxIntronLen_ = maxIntronLen;
minAnchorLen_ = minAnchorLen;
minAnchorLen_noncan_ = minAnchorLen_noncan;
no_spliced_alignment_ = no_spliced_alignment;
transcriptome_mapping_only_ = transcriptome_mapping_only;
transcriptome_assembly_ = transcriptome_assembly;
xs_only_ = xs_only;
avoid_pseudogene_ = avoid_pseudogene;
}
size_t minIntronLen() const { return minIntronLen_; }
size_t maxIntronLen() const { return maxIntronLen_; }
uint32_t minAnchorLen() const { return minAnchorLen_; }
uint32_t minAnchorLen_noncan() const { return minAnchorLen_noncan_; }
bool no_spliced_alignment() const { return no_spliced_alignment_; }
bool transcriptome_mapping_only() const { return transcriptome_mapping_only_; }
bool transcriptome_assembly() const { return transcriptome_assembly_; }
bool xs_only() const { return xs_only_; }
bool avoid_pseudogene() const { return avoid_pseudogene_; }
private:
size_t minIntronLen_;
size_t maxIntronLen_;
// Minimum anchor length required for canonical splice sites
uint32_t minAnchorLen_;
// Minimum anchor length required for non-canonical splice sites
uint32_t minAnchorLen_noncan_;
bool no_spliced_alignment_;
bool transcriptome_mapping_only_;
bool transcriptome_assembly_;
bool xs_only_;
bool avoid_pseudogene_;
};
#endif /*ndef TP_H_*/
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