/usr/include/ngs/Alignment.hpp is in libngs-sdk-dev 1.3.0-2.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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*
* PUBLIC DOMAIN NOTICE
* National Center for Biotechnology Information
*
* This software/database is a "United States Government Work" under the
* terms of the United States Copyright Act. It was written as part of
* the author's official duties as a United States Government employee and
* thus cannot be copyrighted. This software/database is freely available
* to the public for use. The National Library of Medicine and the U.S.
* Government have not placed any restriction on its use or reproduction.
*
* Although all reasonable efforts have been taken to ensure the accuracy
* and reliability of the software and data, the NLM and the U.S.
* Government do not and cannot warrant the performance or results that
* may be obtained by using this software or data. The NLM and the U.S.
* Government disclaim all warranties, express or implied, including
* warranties of performance, merchantability or fitness for any particular
* purpose.
*
* Please cite the author in any work or product based on this material.
*
* ===========================================================================
*
*/
#ifndef _hpp_ngs_alignment_
#define _hpp_ngs_alignment_
#ifndef _hpp_ngs_fragment_
#include <ngs/Fragment.hpp>
#endif
namespace ngs
{
/*----------------------------------------------------------------------
* forwards and typedefs
*/
typedef FragmentRef AlignmentRef;
/*======================================================================
* Alignment
* represents an alignment between a Fragment and Reference sub-sequence
* provides a path to Read and mate Alignment
*/
class Alignment : public Fragment
{
public:
/* getAlignmentId
* retrieve an identifying String that can be used for later access.
* the id will be unique within ReadCollection.
*/
StringRef getAlignmentId () const
throw ( ErrorMsg );
/*------------------------------------------------------------------
* Reference
*/
/* getReferenceSpec
*/
String getReferenceSpec () const
throw ( ErrorMsg );
/* getMappingQuality
*/
int getMappingQuality () const
throw ( ErrorMsg );
/* getReferenceBases
* return reference bases
*/
StringRef getReferenceBases () const
throw ( ErrorMsg );
/*------------------------------------------------------------------
* Fragment
*/
/* getReadGroup
*/
String getReadGroup () const
throw ( ErrorMsg );
/* getReadId
*/
StringRef getReadId () const
throw ( ErrorMsg );
/* getClippedFragmentBases
* return fragment bases
*/
StringRef getClippedFragmentBases () const
throw ( ErrorMsg );
/* getClippedFragmentQualities
* return fragment phred quality values
* using ASCII offset of 33
*/
StringRef getClippedFragmentQualities () const
throw ( ErrorMsg );
/* getAlignedFragmentBases
* return fragment bases in their aligned orientation
*/
StringRef getAlignedFragmentBases () const
throw ( ErrorMsg );
/*------------------------------------------------------------------
* details of this alignment
*/
/* AlignmentFilter
* values should be or'd together to produce filter bits
*/
enum AlignmentFilter
{
passFailed = 1, // reads rejected due to platform/vendor quality criteria
passDuplicates = 2, // either a PCR or optical duplicate
minMapQuality = 4, // pass alignments with mappingQuality >= param
maxMapQuality = 8, // pass alignments with mappingQuality <= param
noWraparound = 16, // do not include leading wrapped around alignments to circular references
startWithinSlice = 32 // change slice intersection criteria so that start pos is within slice
};
/* AlignmentCategory
*/
enum AlignmentCategory
{
primaryAlignment = 1,
secondaryAlignment = 2,
all = primaryAlignment | secondaryAlignment
};
/* getAlignmentCategory
* alignments are categorized as primary or secondary (alternate).
* return an AlignmentCategory
* throws ErrorMsg if the property cannot be retrieved
*/
AlignmentCategory getAlignmentCategory () const
throw ( ErrorMsg );
/* getAlignmentPosition
* retrieve the Alignment's starting position on the Reference
* return 0-based offset from start of Reference
* throws ErrorMsg if the property cannot be retrieved
*/
int64_t getAlignmentPosition () const
throw ( ErrorMsg );
/* getReferencePositionProjectionRange
* retrieve the projection of Reference position on the Alignment
* ref_pos - 0-based offset from start of Reference
* returns a packed 64bit value:
* -upper 32bits represent a 0-based offset from start of the Alignment
* corresponding to ref_pos (beginning of the insertion in the case ref_pos
* projects on the insertion)
* -lower 32bits represent the length of the ref_pos projection on the
* Alignment: e.g. 1 - match/mismatch, 0 - ref_pos is within the
* region deleted from the Alignment, > 1 - there is an insertion
* on the Alignment so ref_pos can be projected anywhere from the
* beginning of that insertion to the end of it.
* throws ErrorMsg if the property cannot be retrieved
*/
uint64_t getReferencePositionProjectionRange ( int64_t ref_pos ) const
throw ( ErrorMsg );
/* getAligmentLength
* retrieve the projected length of an Alignment projected upon Reference.
* return unsigned length of projection
* throws ErrorMsg if the property cannot be retrieved
*/
uint64_t getAlignmentLength () const
throw ( ErrorMsg );
/* getIsReversedOrientation
* test if orientation is reversed with respect to the Reference sequence.
* return true if reversed
* throws ErrorMsg if the property cannot be retrieved
*/
bool getIsReversedOrientation () const
throw ( ErrorMsg );
/* ClipEdge
*/
enum ClipEdge
{
clipLeft = 0,
clipRight = 1
};
/* getSoftClip
*/
int getSoftClip ( ClipEdge edge ) const
throw ( ErrorMsg );
/* getTemplateLength
*/
uint64_t getTemplateLength () const
throw ( ErrorMsg );
/* getShortCigar
* returns a text string describing alignment details
*/
StringRef getShortCigar ( bool clipped ) const
throw ( ErrorMsg );
/* getLongCigar
* returns a text string describing alignment details
*/
StringRef getLongCigar ( bool clipped ) const
throw ( ErrorMsg );
/* getRNAOrientation
* returns '+' if positive strand is transcribed
* returns '-' if negative strand is transcribed
* returns '?' if unknown
*/
char getRNAOrientation () const
throw ( ErrorMsg );
/*------------------------------------------------------------------
* details of mate alignment
*/
/* hasMate
*/
bool hasMate () const
throw ();
/* getMateAlignmentId
*/
StringRef getMateAlignmentId () const
throw ( ErrorMsg );
/* getMateAlignment
*/
Alignment getMateAlignment () const
throw ( ErrorMsg );
/* getMateReferenceSpec
*/
String getMateReferenceSpec () const
throw ( ErrorMsg );
/* getMateIsReversedOrientation
*/
bool getMateIsReversedOrientation () const
throw ( ErrorMsg );
public:
// C++ support
Alignment & operator = ( AlignmentRef ref )
throw ();
Alignment ( AlignmentRef ref )
throw ();
Alignment & operator = ( const Alignment & obj )
throw ( ErrorMsg );
Alignment ( const Alignment & obj )
throw ( ErrorMsg );
~ Alignment ()
throw ();
};
} // namespace ngs
// inlines
#ifndef _inl_ngs_alignment_
#include <ngs/inl/Alignment.hpp>
#endif
#endif // _hpp_ngs_alignment_
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