libStatGen Software
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SamInterface.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 __SAM_INTERFACE_H__
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#define __SAM_INTERFACE_H__
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#include "GenericSamInterface.h"
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class
SamInterface
:
public
GenericSamInterface
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{
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public
:
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SamInterface
();
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~
SamInterface
();
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// Reads the header section from the specified SAM file and stores it in
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// the passed in header.
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virtual
bool
readHeader(
IFILE
filePtr,
SamFileHeader
& header,
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SamStatus
& status);
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// Writes the specified header into the specified SAM file.
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virtual
bool
writeHeader(
IFILE
filePtr,
SamFileHeader
& header,
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SamStatus
& status);
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// Reads the next record from the specified SAM file and stores it in
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// the passed in record.
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virtual
void
readRecord(
IFILE
filePtr,
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SamFileHeader
& header,
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SamRecord
& record,
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SamStatus
& samStatus);
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// Writes the specified record into the specified SAM file.
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virtual
SamStatus::Status
writeRecord(
IFILE
filePtr,
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SamFileHeader
& header,
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SamRecord
& record,
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SamRecord::SequenceTranslation
translation);
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private
:
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void
ParseHeaderLine(
StringIntHash
& tags,
StringArray
& values);
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String
buffer;
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StringArray
tokens;
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// Store the first record as it is read when trying to read the
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// header so it can be returned when a record is read.
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// Clear after it has been processed.
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String
myFirstRecord;
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};
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#endif
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SamRecord::SequenceTranslation
SequenceTranslation
Enum containing the settings on how to translate the sequence if a reference is available.
Definition:
SamRecord.h:57
String
Definition:
StringBasics.h:38
StatGenStatus
This class is used to track the status results of some methods in the BAM classes.
Definition:
StatGenStatus.h:26
StringIntHash
Definition:
StringHash.h:193
StatGenStatus::Status
Status
Return value enum for StatGenFile methods.
Definition:
StatGenStatus.h:31
SamFileHeader
This class allows a user to get/set the fields in a SAM/BAM Header.
Definition:
SamFileHeader.h:34
SamRecord
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
Definition:
SamRecord.h:51
GenericSamInterface
Definition:
GenericSamInterface.h:26
SamInterface
Definition:
SamInterface.h:23
InputFile
Class for easily reading/writing files without having to worry about file type (uncompressed,...
Definition:
InputFile.h:36
StringArray
Definition:
StringArray.h:23
bam
SamInterface.h
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