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/*
* Copyright (C) 2012-2013 Regents of the University of Michigan
*
* This program 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.
*
* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
*/
#ifndef __TABIX_H__
#define __TABIX_H__
#include <stdint.h>
#include <vector>
#include <map>
#include <stdlib.h>
#include "IndexBase.h"
#include "InputFile.h"
#include "StatGenStatus.h"
class Tabix : public IndexBase
{
public:
enum Format
{
FORMAT_GENERIC = 0,
FORMAT_SAM = 1,
FORMAT_VCF = 2
};
Tabix();
virtual ~Tabix();
/// Reset the member data for a new index file.
void resetIndex();
// Read & parse the specified index file.
/// \param filename the bam index file to be read.
/// \return the status of the read.
StatGenStatus::Status readIndex(const char* filename);
/// Get the starting file offset to look for the specified start position.
/// For an entire reference ID, set start to -1.
/// To start at the beginning of the region, set start to 0/-1.
bool getStartPos(const char* refName, int32_t start,
uint64_t& fileStartPos) const;
/// Return the reference name at the specified index or
/// throws an exception if out of range.
const char* getRefName(unsigned int indexNum) const;
// Get the format of this tabix file.
inline int32_t getFormat() const { return myFormat.format; }
private:
struct TabixFormat
{
int32_t format;
int32_t col_seq;
int32_t col_beg;
int32_t col_end;
int32_t meta; // character that starts header lines
int32_t skip; // Number of lines to skip from putting into the index.
};
TabixFormat myFormat;
char* myChromNamesBuffer;
// vector pointing to the chromosome names.
std::vector<const char*> myChromNamesVector;
};
#endif
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