libStatGen Software
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GenericSamInterface.h
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/*
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* Copyright (C) 2010 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 __GENERIC_SAM_INTERFACE_H__
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#define __GENERIC_SAM_INTERFACE_H__
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#include "SamStatus.h"
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#include "
InputFile.h
"
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#include "SamFileHeader.h"
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#include "SamRecord.h"
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class
GenericSamInterface
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{
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public
:
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GenericSamInterface
();
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virtual
~
GenericSamInterface
();
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// Pure virtual method that reads the header section from the specified file
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// and stores it in the passed in header, returns false and sets the status
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// on failure.
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// Will be implemented specifically for sam/bam files.
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virtual
bool
readHeader(
IFILE
filePtr,
SamFileHeader
& header,
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SamStatus
& status) = 0;
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// Pure virtual method that writes the specified header into the specified
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// file, returns false and sets the status on failure.
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// Will be implemented specifically for sam/bam files.
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virtual
bool
writeHeader(
IFILE
filePtr,
SamFileHeader
& header,
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SamStatus
& status) = 0;
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// Pure virtual method that reads the next record from the specified file
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// and stores it in the passed in record.
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// Will be implemented specifically for sam/bam files.
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// TODO On error, a more detailed message is appended to statusMsg.
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virtual
void
readRecord(
IFILE
filePtr,
SamFileHeader
& header,
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SamRecord
& record,
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SamStatus
& samStatus) = 0;
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// Pure virtual method that writes the specified record into the specified
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// file.
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// Will be implemented specifically for sam/bam files.
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virtual
SamStatus::Status
writeRecord(
IFILE
filePtr,
SamFileHeader
& header,
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SamRecord
& record,
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SamRecord::SequenceTranslation
translation) = 0;
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};
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#endif
SamRecord::SequenceTranslation
SequenceTranslation
Enum containing the settings on how to translate the sequence if a reference is available.
Definition:
SamRecord.h:57
StatGenStatus
This class is used to track the status results of some methods in the BAM classes.
Definition:
StatGenStatus.h:27
StatGenStatus::Status
Status
Return value enum for StatGenFile methods.
Definition:
StatGenStatus.h:32
InputFile.h
SamFileHeader
This class allows a user to get/set the fields in a SAM/BAM Header.
Definition:
SamFileHeader.h:35
SamRecord
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
Definition:
SamRecord.h:52
GenericSamInterface
Definition:
GenericSamInterface.h:27
InputFile
Class for easily reading/writing files without having to worry about file type (uncompressed,...
Definition:
InputFile.h:37
bam
GenericSamInterface.h
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