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CBamDb::SPileupValues Struct Reference

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#include <sra/readers/bam/bamread.hpp>

+ Collaboration diagram for CBamDb::SPileupValues:

Classes

struct  SCountACGT
 

Public Types

enum  {
  kStat_A = 0 , kStat_C = 1 , kStat_G = 2 , kStat_T = 3 ,
  kStat_Gap = 4 , kStat_Match = 5 , kStat_Intron = 6 , kNumStat_ACGT = 4 ,
  kNumStat = 7
}
 
enum  EIntronMode { eNoCountIntron , eCountIntron }
 
typedef Uint4 TCount
 

Public Member Functions

bool count_introns () const
 
 SPileupValues ()
 
 SPileupValues (CRange< TSeqPos > ref_range, EIntronMode intron_mode=eNoCountIntron)
 
void initialize (CRange< TSeqPos > ref_range, EIntronMode intron_mode=eNoCountIntron)
 
void finalize (ICollectPileupCallback *callback)
 
const TCountget_acgt_counts () const
 
void make_split_acgt (TSeqPos len)
 
const TCountget_split_acgt_counts (int k, TSeqPos len) const
 
const TCountget_match_counts () const
 
const TCountget_gap_counts () const
 
const TCountget_intron_counts () const
 
void add_match_graph_pos (TSeqPos pos)
 
void add_match_graph_range (TSeqPos pos, TSeqPos end)
 
void add_gap_graph_range (TSeqPos pos, TSeqPos end)
 
void add_intron_graph_range (TSeqPos pos, TSeqPos end)
 
void add_bases_graph_range (TSeqPos pos, TSeqPos end, CTempString read, TSeqPos read_pos)
 
void add_bases_graph_range_raw (TSeqPos pos, TSeqPos end, CTempString read, TSeqPos read_pos)
 
void decode_gap (TSeqPos len)
 
void decode_intron (TSeqPos len)
 
void advance_current_beg (TSeqPos ref_pos, ICollectPileupCallback *callback)
 
void advance_current_end (TSeqPos ref_end)
 
void update_current_ref_start (TSeqPos ref_pos, ICollectPileupCallback *callback)
 
bool trim_ref_range (TSeqPos &ref_pos, TSeqPos &ref_end)
 
bool trim_ref_range (TSeqPos &ref_pos, TSeqPos &ref_end, TSeqPos &read_pos)
 
void add_match_ref_range (TSeqPos ref_pos, TSeqPos ref_end)
 
void add_gap_ref_range (TSeqPos ref_pos, TSeqPos ref_end)
 
void add_intron_ref_range (TSeqPos ref_pos, TSeqPos ref_end)
 
void add_bases_ref_range (TSeqPos ref_pos, TSeqPos ref_end, const CTempString &read, TSeqPos read_pos)
 
void add_bases_ref_range_raw (TSeqPos ref_pos, TSeqPos ref_end, const CTempString &read, TSeqPos read_pos)
 
void update_max_counts (TSeqPos len)
 
TCount get_max_count (int type) const
 

Public Attributes

TSeqPos m_RefFrom
 
TSeqPos m_RefToOpen
 
TSeqPos m_RefStop
 
TSeqPos m_SplitACGTLen
 
EIntronMode m_IntronMode
 
CSimpleBufferT< SCountACGTcc_acgt
 
CSimpleBufferT< TCountcc_split_acgt [kNumStat_ACGT]
 
CSimpleBufferT< TCountcc_gap
 
CSimpleBufferT< TCountcc_match
 
CSimpleBufferT< TCountcc_intron
 
TCount max_count [kNumStat]
 

Static Public Attributes

static const TSeqPos FLUSH_SIZE = 512
 

Detailed Description

Definition at line 293 of file bamread.hpp.

Member Typedef Documentation

◆ TCount

Definition at line 295 of file bamread.hpp.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum
Enumerator
kStat_A 
kStat_C 
kStat_G 
kStat_T 
kStat_Gap 
kStat_Match 
kStat_Intron 
kNumStat_ACGT 
kNumStat 

Definition at line 297 of file bamread.hpp.

◆ EIntronMode

Enumerator
eNoCountIntron 
eCountIntron 

Definition at line 309 of file bamread.hpp.

Constructor & Destructor Documentation

◆ SPileupValues() [1/2]

CBamDb::SPileupValues::SPileupValues ( )

◆ SPileupValues() [2/2]

CBamDb::SPileupValues::SPileupValues ( CRange< TSeqPos ref_range,
EIntronMode  intron_mode = eNoCountIntron 
)
explicit

Member Function Documentation

◆ add_bases_graph_range()

void CBamDb::SPileupValues::add_bases_graph_range ( TSeqPos  pos,
TSeqPos  end,
CTempString  read,
TSeqPos  read_pos 
)

Referenced by add_bases_ref_range().

◆ add_bases_graph_range_raw()

void CBamDb::SPileupValues::add_bases_graph_range_raw ( TSeqPos  pos,
TSeqPos  end,
CTempString  read,
TSeqPos  read_pos 
)

Referenced by add_bases_ref_range_raw().

◆ add_bases_ref_range()

void CBamDb::SPileupValues::add_bases_ref_range ( TSeqPos  ref_pos,
TSeqPos  ref_end,
const CTempString read,
TSeqPos  read_pos 
)
inline

Definition at line 467 of file bamread.hpp.

References add_bases_graph_range(), m_RefFrom, and trim_ref_range().

◆ add_bases_ref_range_raw()

void CBamDb::SPileupValues::add_bases_ref_range_raw ( TSeqPos  ref_pos,
TSeqPos  ref_end,
const CTempString read,
TSeqPos  read_pos 
)
inline

Definition at line 476 of file bamread.hpp.

References add_bases_graph_range_raw(), m_RefFrom, and trim_ref_range().

◆ add_gap_graph_range()

void CBamDb::SPileupValues::add_gap_graph_range ( TSeqPos  pos,
TSeqPos  end 
)
inline

Definition at line 378 of file bamread.hpp.

References _ASSERT, and cc_gap.

Referenced by add_gap_ref_range().

◆ add_gap_ref_range()

void CBamDb::SPileupValues::add_gap_ref_range ( TSeqPos  ref_pos,
TSeqPos  ref_end 
)
inline

Definition at line 453 of file bamread.hpp.

References add_gap_graph_range(), m_RefFrom, and trim_ref_range().

◆ add_intron_graph_range()

void CBamDb::SPileupValues::add_intron_graph_range ( TSeqPos  pos,
TSeqPos  end 
)
inline

Definition at line 384 of file bamread.hpp.

References _ASSERT, and cc_intron.

Referenced by add_intron_ref_range().

◆ add_intron_ref_range()

void CBamDb::SPileupValues::add_intron_ref_range ( TSeqPos  ref_pos,
TSeqPos  ref_end 
)
inline

Definition at line 460 of file bamread.hpp.

References add_intron_graph_range(), count_introns(), m_RefFrom, and trim_ref_range().

◆ add_match_graph_pos()

void CBamDb::SPileupValues::add_match_graph_pos ( TSeqPos  pos)
inline

Definition at line 368 of file bamread.hpp.

References cc_match.

◆ add_match_graph_range()

void CBamDb::SPileupValues::add_match_graph_range ( TSeqPos  pos,
TSeqPos  end 
)
inline

Definition at line 372 of file bamread.hpp.

References cc_match.

Referenced by add_match_ref_range().

◆ add_match_ref_range()

void CBamDb::SPileupValues::add_match_ref_range ( TSeqPos  ref_pos,
TSeqPos  ref_end 
)
inline

Definition at line 446 of file bamread.hpp.

References add_match_graph_range(), m_RefFrom, and trim_ref_range().

◆ advance_current_beg()

void CBamDb::SPileupValues::advance_current_beg ( TSeqPos  ref_pos,
ICollectPileupCallback callback 
)

◆ advance_current_end()

void CBamDb::SPileupValues::advance_current_end ( TSeqPos  ref_end)

Referenced by trim_ref_range().

◆ count_introns()

bool CBamDb::SPileupValues::count_introns ( ) const
inline

Definition at line 320 of file bamread.hpp.

References eNoCountIntron, and m_IntronMode.

Referenced by add_intron_ref_range().

◆ decode_gap()

void CBamDb::SPileupValues::decode_gap ( TSeqPos  len)

◆ decode_intron()

void CBamDb::SPileupValues::decode_intron ( TSeqPos  len)

◆ finalize()

void CBamDb::SPileupValues::finalize ( ICollectPileupCallback callback)

◆ get_acgt_counts()

const TCount* CBamDb::SPileupValues::get_acgt_counts ( ) const
inline

Definition at line 343 of file bamread.hpp.

References cc_acgt.

◆ get_gap_counts()

const TCount* CBamDb::SPileupValues::get_gap_counts ( ) const
inline

Definition at line 359 of file bamread.hpp.

References cc_gap, and CSimpleBufferT< T, ResizeStrategy >::data().

◆ get_intron_counts()

const TCount* CBamDb::SPileupValues::get_intron_counts ( ) const
inline

Definition at line 363 of file bamread.hpp.

References cc_intron, and CSimpleBufferT< T, ResizeStrategy >::data().

◆ get_match_counts()

const TCount* CBamDb::SPileupValues::get_match_counts ( ) const
inline

Definition at line 355 of file bamread.hpp.

References cc_match, and CSimpleBufferT< T, ResizeStrategy >::data().

◆ get_max_count()

TCount CBamDb::SPileupValues::get_max_count ( int  type) const
inline

Definition at line 488 of file bamread.hpp.

References max_count, and type.

◆ get_split_acgt_counts()

const TCount* CBamDb::SPileupValues::get_split_acgt_counts ( int  k,
TSeqPos  len 
) const
inline

◆ initialize()

void CBamDb::SPileupValues::initialize ( CRange< TSeqPos ref_range,
EIntronMode  intron_mode = eNoCountIntron 
)

◆ make_split_acgt()

void CBamDb::SPileupValues::make_split_acgt ( TSeqPos  len)

Referenced by get_split_acgt_counts().

◆ trim_ref_range() [1/2]

bool CBamDb::SPileupValues::trim_ref_range ( TSeqPos ref_pos,
TSeqPos ref_end 
)
inline

◆ trim_ref_range() [2/2]

bool CBamDb::SPileupValues::trim_ref_range ( TSeqPos ref_pos,
TSeqPos ref_end,
TSeqPos read_pos 
)
inline

Definition at line 426 of file bamread.hpp.

References _ASSERT, advance_current_end(), m_RefFrom, m_RefStop, and m_RefToOpen.

◆ update_current_ref_start()

void CBamDb::SPileupValues::update_current_ref_start ( TSeqPos  ref_pos,
ICollectPileupCallback callback 
)
inline

Definition at line 402 of file bamread.hpp.

References advance_current_beg(), FLUSH_SIZE, m_RefFrom, and m_RefToOpen.

◆ update_max_counts()

void CBamDb::SPileupValues::update_max_counts ( TSeqPos  len)

Member Data Documentation

◆ cc_acgt

CSimpleBufferT<SCountACGT> CBamDb::SPileupValues::cc_acgt

Definition at line 328 of file bamread.hpp.

Referenced by get_acgt_counts().

◆ cc_gap

CSimpleBufferT<TCount> CBamDb::SPileupValues::cc_gap

Definition at line 330 of file bamread.hpp.

Referenced by add_gap_graph_range(), and get_gap_counts().

◆ cc_intron

CSimpleBufferT<TCount> CBamDb::SPileupValues::cc_intron

Definition at line 332 of file bamread.hpp.

Referenced by add_intron_graph_range(), and get_intron_counts().

◆ cc_match

CSimpleBufferT<TCount> CBamDb::SPileupValues::cc_match

Definition at line 331 of file bamread.hpp.

Referenced by add_match_graph_pos(), add_match_graph_range(), and get_match_counts().

◆ cc_split_acgt

CSimpleBufferT<TCount> CBamDb::SPileupValues::cc_split_acgt[kNumStat_ACGT]

Definition at line 329 of file bamread.hpp.

Referenced by get_split_acgt_counts().

◆ FLUSH_SIZE

const TSeqPos CBamDb::SPileupValues::FLUSH_SIZE = 512
static

Definition at line 395 of file bamread.hpp.

Referenced by update_current_ref_start().

◆ m_IntronMode

EIntronMode CBamDb::SPileupValues::m_IntronMode

Definition at line 318 of file bamread.hpp.

Referenced by count_introns().

◆ m_RefFrom

TSeqPos CBamDb::SPileupValues::m_RefFrom

◆ m_RefStop

TSeqPos CBamDb::SPileupValues::m_RefStop

Definition at line 316 of file bamread.hpp.

Referenced by trim_ref_range().

◆ m_RefToOpen

TSeqPos CBamDb::SPileupValues::m_RefToOpen

Definition at line 315 of file bamread.hpp.

Referenced by trim_ref_range(), and update_current_ref_start().

◆ m_SplitACGTLen

TSeqPos CBamDb::SPileupValues::m_SplitACGTLen

Definition at line 317 of file bamread.hpp.

Referenced by get_split_acgt_counts().

◆ max_count

TCount CBamDb::SPileupValues::max_count[kNumStat]

Definition at line 333 of file bamread.hpp.

Referenced by get_max_count().


The documentation for this struct was generated from the following file:
Modified on Wed Apr 24 14:19:02 2024 by modify_doxy.py rev. 669887