libStatGen Software
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Tabix.h
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/*
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* Copyright (C) 2012-2013 Regents of the University of Michigan
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*
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* This program 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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* This program 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 this program. If not, see <http://www.gnu.org/licenses/>.
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*/
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#ifndef __TABIX_H__
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#define __TABIX_H__
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#include <stdint.h>
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#include <vector>
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#include <map>
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#include <stdlib.h>
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#include "IndexBase.h"
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#include "
InputFile.h
"
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#include "StatGenStatus.h"
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class
Tabix
:
public
IndexBase
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{
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public
:
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enum
Format
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{
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FORMAT_GENERIC = 0,
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FORMAT_SAM = 1,
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FORMAT_VCF = 2
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};
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Tabix
();
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virtual
~
Tabix
();
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/// Reset the member data for a new index file.
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void
resetIndex
();
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// Read & parse the specified index file.
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/// \param filename the bam index file to be read.
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/// \return the status of the read.
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StatGenStatus::Status
readIndex
(
const
char
* filename);
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/// Get the starting file offset to look for the specified start position.
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/// For an entire reference ID, set start to -1.
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/// To start at the beginning of the region, set start to 0/-1.
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bool
getStartPos
(
const
char
* refName, int32_t start,
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uint64_t& fileStartPos)
const
;
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/// Return the reference name at the specified index or
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/// throws an exception if out of range.
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const
char
*
getRefName
(
unsigned
int
indexNum)
const
;
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// Get the format of this tabix file.
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inline
int32_t getFormat()
const
{
return
myFormat.format; }
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private
:
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struct
TabixFormat
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{
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int32_t format;
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int32_t col_seq;
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int32_t col_beg;
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int32_t col_end;
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int32_t meta;
// character that starts header lines
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int32_t skip;
// Number of lines to skip from putting into the index.
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};
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TabixFormat myFormat;
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char
* myChromNamesBuffer;
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// vector pointing to the chromosome names.
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std::vector<const char*> myChromNamesVector;
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};
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#endif
Tabix::getStartPos
bool getStartPos(const char *refName, int32_t start, uint64_t &fileStartPos) const
Get the starting file offset to look for the specified start position.
Definition:
Tabix.cpp:218
Tabix::getRefName
const char * getRefName(unsigned int indexNum) const
Return the reference name at the specified index or throws an exception if out of range.
Definition:
Tabix.cpp:247
IndexBase
Definition:
IndexBase.h:63
StatGenStatus::Status
Status
Return value enum for StatGenFile methods.
Definition:
StatGenStatus.h:32
InputFile.h
Tabix
Definition:
Tabix.h:32
Tabix::resetIndex
void resetIndex()
Reset the member data for a new index file.
Definition:
Tabix.cpp:39
Tabix::readIndex
StatGenStatus::Status readIndex(const char *filename)
Definition:
Tabix.cpp:52
general
Tabix.h
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