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Cigar Class Reference

This class represents the CIGAR without any methods to set the cigar (see CigarRoller for that). More...

#include <Cigar.h>

Inheritance diagram for Cigar:
Collaboration diagram for Cigar:

Classes

struct  CigarOperator
 

Public Types

enum  Operation {
  none =0 , match , mismatch , insert ,
  del , skip , softClip , hardClip ,
  pad
}
 Enum for the cigar operations. More...
 

Public Member Functions

 Cigar ()
 Default constructor initializes as a CIGAR with no operations.
 
void getCigarString (String &cigarString) const
 Set the passed in String to the string reprentation of the Cigar operations in this object.
 
void getCigarString (std::string &cigarString) const
 Set the passed in std::string to the string reprentation of the Cigar operations in this object.
 
void getExpandedString (std::string &s) const
 Sets the specified string to a valid CIGAR string of characters that represent the cigar with no digits (a CIGAR of "3M" would return "MMM").
 
const CigarOperatoroperator[] (int i) const
 Return the Cigar Operation at the specified index (starting at 0).
 
const CigarOperatorgetOperator (int i) const
 Return the Cigar Operation at the specified index (starting at 0).
 
bool operator== (Cigar &rhs) const
 Return true if the 2 Cigars are the same (the same operations of the same sizes).
 
int size () const
 Return the number of cigar operations.
 
void Dump () const
 Write this object as a string to cout.
 
int getExpectedQueryBaseCount () const
 Return the length of the read that corresponds to the current CIGAR string.
 
int getExpectedReferenceBaseCount () const
 Return the number of bases in the reference that this CIGAR "spans".
 
int getNumBeginClips () const
 Return the number of clips that are at the beginning of the cigar.
 
int getNumEndClips () const
 Return the number of clips that are at the end of the cigar.
 
int32_t getRefOffset (int32_t queryIndex)
 Return the reference offset associated with the specified query index or INDEX_NA based on this cigar.
 
int32_t getQueryIndex (int32_t refOffset)
 Return the query index associated with the specified reference offset or INDEX_NA based on this cigar.
 
int32_t getRefPosition (int32_t queryIndex, int32_t queryStartPos)
 Return the reference position associated with the specified query index or INDEX_NA based on this cigar and the specified queryStartPos which is the leftmost mapping position of the first matching base in the query.
 
int32_t getQueryIndex (int32_t refPosition, int32_t queryStartPos)
 Return the query index or INDEX_NA associated with the specified reference offset when the query starts at the specified reference position.
 
int32_t getExpandedCigarIndexFromQueryIndex (int32_t queryIndex)
 Returns the index into the expanded cigar for the cigar associated with the specified queryIndex.
 
int32_t getExpandedCigarIndexFromRefOffset (int32_t refOffset)
 Returns the index into the expanded cigar for the cigar associated with the specified reference offset.
 
int32_t getExpandedCigarIndexFromRefPos (int32_t refPosition, int32_t queryStartPos)
 Returns the index into the expanded cigar for the cigar associated with the specified reference position and queryStartPos.
 
char getCigarCharOp (int32_t expandedCigarIndex)
 Return the character code of the cigar operator associated with the specified expanded CIGAR index.
 
char getCigarCharOpFromQueryIndex (int32_t queryIndex)
 Return the character code of the cigar operator associated with the specified queryIndex.
 
char getCigarCharOpFromRefOffset (int32_t refOffset)
 Return the character code of the cigar operator associated with the specified reference offset.
 
char getCigarCharOpFromRefPos (int32_t refPosition, int32_t queryStartPos)
 Return the character code of the cigar operator associated with the specified reference position.
 
uint32_t getNumOverlaps (int32_t start, int32_t end, int32_t queryStartPos)
 Return the number of bases that overlap the reference and the read associated with this cigar that falls within the specified region.
 
bool hasIndel ()
 Return whether or not the cigar has indels (insertions or delections)
 

Static Public Member Functions

static bool foundInReference (Operation op)
 Return true if the specified operation is found in the reference sequence, false if not.
 
static bool foundInReference (char op)
 Return true if the specified operation is found in the reference sequence, false if not.
 
static bool foundInReference (const CigarOperator &op)
 Return true if the specified operation is found in the reference sequence, false if not.
 
static bool foundInQuery (Operation op)
 Return true if the specified operation is found in the query sequence, false if not.
 
static bool foundInQuery (char op)
 Return true if the specified operation is found in the query sequence, false if not.
 
static bool foundInQuery (const CigarOperator &op)
 Return true if the specified operation is found in the query sequence, false if not.
 
static bool isClip (Operation op)
 Return true if the specified operation is a clipping operation, false if not.
 
static bool isClip (char op)
 Return true if the specified operation is a clipping operation, false if not.
 
static bool isClip (const CigarOperator &op)
 Return true if the specified operation is a clipping operation, false if not.
 
static bool isMatchOrMismatch (Operation op)
 Return true if the specified operation is a match/mismatch operation, false if not.
 
static bool isMatchOrMismatch (const CigarOperator &op)
 Return true if the specified operation is a match/mismatch operation, false if not.
 

Static Public Attributes

static const int MAX_OP_VALUE = pad
 
static const int32_t INDEX_NA = -1
 Value associated with an index that is not applicable/does not exist, used for converting between query and reference indexes/offsets when an associated index/offset does not exist.
 

Protected Member Functions

void clearQueryAndReferenceIndexes ()
 
void setQueryAndReferenceIndexes ()
 

Protected Attributes

std::vector< CigarOperatorcigarOperations
 

Friends

std::ostream & operator<< (std::ostream &stream, const Cigar &cigar)
 Writes all of the cigar operations contained in the cigar to the passed in stream.
 

Detailed Description

This class represents the CIGAR without any methods to set the cigar (see CigarRoller for that).

This class represents the CIGAR. It contains methods for converting to strings and extracting information from the cigar on how a read maps to the reference.

It only contains read only methods. There are no ways to set values. To set a value, a child class must be used.

Definition at line 83 of file Cigar.h.

Member Enumeration Documentation

◆ Operation

Enum for the cigar operations.

Enumerator
none 

no operation has been set.

match 

match/mismatch operation. Associated with CIGAR Operation "M"

mismatch 

mismatch operation. Associated with CIGAR Operation "M"

insert 

insertion to the reference (the query sequence contains bases that have no corresponding base in the reference). Associated with CIGAR Operation "I"

del 

deletion from the reference (the reference contains bases that have no corresponding base in the query sequence). Associated with CIGAR Operation "D"

skip 

skipped region from the reference (the reference contains bases that have no corresponding base in the query sequence). Associated with CIGAR Operation "N"

softClip 

Soft clip on the read (clipped sequence present in the query sequence, but not in reference). Associated with CIGAR Operation "S".

hardClip 

Hard clip on the read (clipped sequence not present in the query sequence or reference). Associated with CIGAR Operation "H".

pad 

Padding (not in reference or query). Associated with CIGAR Operation "P".

Definition at line 87 of file Cigar.h.

87 {
88 none=0, ///< no operation has been set.
89 match, ///< match/mismatch operation. Associated with CIGAR Operation "M"
90 mismatch, ///< mismatch operation. Associated with CIGAR Operation "M"
91 insert, ///< insertion to the reference (the query sequence contains bases that have no corresponding base in the reference). Associated with CIGAR Operation "I"
92 del, ///< deletion from the reference (the reference contains bases that have no corresponding base in the query sequence). Associated with CIGAR Operation "D"
93 skip, ///< skipped region from the reference (the reference contains bases that have no corresponding base in the query sequence). Associated with CIGAR Operation "N"
94 softClip, ///< Soft clip on the read (clipped sequence present in the query sequence, but not in reference). Associated with CIGAR Operation "S"
95 hardClip, ///< Hard clip on the read (clipped sequence not present in the query sequence or reference). Associated with CIGAR Operation "H"
96 pad ///< Padding (not in reference or query). Associated with CIGAR Operation "P"
97 };
@ del
deletion from the reference (the reference contains bases that have no corresponding base in the quer...
Definition Cigar.h:92
@ mismatch
mismatch operation. Associated with CIGAR Operation "M"
Definition Cigar.h:90
@ hardClip
Hard clip on the read (clipped sequence not present in the query sequence or reference)....
Definition Cigar.h:95
@ match
match/mismatch operation. Associated with CIGAR Operation "M"
Definition Cigar.h:89
@ pad
Padding (not in reference or query). Associated with CIGAR Operation "P".
Definition Cigar.h:96
@ insert
insertion to the reference (the query sequence contains bases that have no corresponding base in the ...
Definition Cigar.h:91
@ skip
skipped region from the reference (the reference contains bases that have no corresponding base in th...
Definition Cigar.h:93
@ softClip
Soft clip on the read (clipped sequence present in the query sequence, but not in reference)....
Definition Cigar.h:94
@ none
no operation has been set.
Definition Cigar.h:88

Constructor & Destructor Documentation

◆ Cigar()

Cigar::Cigar ( )
inline

Default constructor initializes as a CIGAR with no operations.

Definition at line 326 of file Cigar.h.

327 {
328 clearQueryAndReferenceIndexes();
329 }

Member Function Documentation

◆ clearQueryAndReferenceIndexes()

void Cigar::clearQueryAndReferenceIndexes ( )
protected

Definition at line 415 of file Cigar.cpp.

416{
417 queryToRef.clear();
418 refToQuery.clear();
419 refToCigar.clear();
420 queryToCigar.clear();
421 myExpandedCigar.clear();
422}

◆ Dump()

void Cigar::Dump ( ) const
inline

Write this object as a string to cout.

Definition at line 370 of file Cigar.h.

371 {
372 String cigarString;
373 getCigarString(cigarString);
374 std::cout << cigarString ;
375 }
void getCigarString(String &cigarString) const
Set the passed in String to the string reprentation of the Cigar operations in this object.
Definition Cigar.cpp:52

References getCigarString().

◆ foundInQuery() [1/3]

static bool Cigar::foundInQuery ( char  op)
inlinestatic

Return true if the specified operation is found in the query sequence, false if not.

Definition at line 236 of file Cigar.h.

237 {
238 switch(op)
239 {
240 case 'M':
241 case '=':
242 case 'X':
243 case 'I':
244 case 'S':
245 return true;
246 default:
247 return false;
248 }
249 return false;
250 }

◆ foundInQuery() [2/3]

static bool Cigar::foundInQuery ( const CigarOperator op)
inlinestatic

Return true if the specified operation is found in the query sequence, false if not.

Definition at line 254 of file Cigar.h.

255 {
256 return(foundInQuery(op.operation));
257 }
static bool foundInQuery(Operation op)
Return true if the specified operation is found in the query sequence, false if not.
Definition Cigar.h:219

References foundInQuery().

◆ foundInQuery() [3/3]

static bool Cigar::foundInQuery ( Operation  op)
inlinestatic

Return true if the specified operation is found in the query sequence, false if not.

Definition at line 219 of file Cigar.h.

220 {
221 switch(op)
222 {
223 case match:
224 case mismatch:
225 case insert:
226 case softClip:
227 return true;
228 default:
229 return false;
230 }
231 return false;
232 }

References insert, match, mismatch, and softClip.

Referenced by foundInQuery(), SamRecord::shiftIndelsLeft(), SamFilter::softClip(), CigarHelper::softClipBeginByRefPos(), and CigarHelper::softClipEndByRefPos().

◆ foundInReference() [1/3]

static bool Cigar::foundInReference ( char  op)
inlinestatic

Return true if the specified operation is found in the reference sequence, false if not.

Definition at line 194 of file Cigar.h.

195 {
196 switch(op)
197 {
198 case 'M':
199 case '=':
200 case 'X':
201 case 'D':
202 case 'N':
203 return true;
204 default:
205 return false;
206 }
207 return false;
208 }

◆ foundInReference() [2/3]

static bool Cigar::foundInReference ( const CigarOperator op)
inlinestatic

Return true if the specified operation is found in the reference sequence, false if not.

Definition at line 212 of file Cigar.h.

213 {
214 return(foundInReference(op.operation));
215 }
static bool foundInReference(Operation op)
Return true if the specified operation is found in the reference sequence, false if not.
Definition Cigar.h:177

References foundInReference().

◆ foundInReference() [3/3]

static bool Cigar::foundInReference ( Operation  op)
inlinestatic

Return true if the specified operation is found in the reference sequence, false if not.

Definition at line 177 of file Cigar.h.

178 {
179 switch(op)
180 {
181 case match:
182 case mismatch:
183 case del:
184 case skip:
185 return true;
186 default:
187 return false;
188 }
189 return false;
190 }

References del, match, mismatch, and skip.

Referenced by foundInReference(), CigarHelper::softClipBeginByRefPos(), and CigarHelper::softClipEndByRefPos().

◆ getCigarCharOp()

char Cigar::getCigarCharOp ( int32_t  expandedCigarIndex)

Return the character code of the cigar operator associated with the specified expanded CIGAR index.

'?' is returned for an out of range index.

Definition at line 295 of file Cigar.cpp.

296{
297 // Check if the expanded cigar has been set yet
298 if ((queryToRef.size() == 0) || (refToQuery.size() == 0))
299 {
300 // Set the expanded cigar.
301 setQueryAndReferenceIndexes();
302 }
303
304 // Check to see if the index is in range.
305 if((expandedCigarIndex < 0) ||
306 ((uint32_t)expandedCigarIndex >= myExpandedCigar.length()))
307 {
308 return('?');
309 }
310 return(myExpandedCigar[expandedCigarIndex]);
311}

Referenced by getCigarCharOpFromQueryIndex(), getCigarCharOpFromRefOffset(), and getCigarCharOpFromRefPos().

◆ getCigarCharOpFromQueryIndex()

char Cigar::getCigarCharOpFromQueryIndex ( int32_t  queryIndex)

Return the character code of the cigar operator associated with the specified queryIndex.

'?' is returned for an out of range index.

Definition at line 314 of file Cigar.cpp.

315{
317}
char getCigarCharOp(int32_t expandedCigarIndex)
Return the character code of the cigar operator associated with the specified expanded CIGAR index.
Definition Cigar.cpp:295
int32_t getExpandedCigarIndexFromQueryIndex(int32_t queryIndex)
Returns the index into the expanded cigar for the cigar associated with the specified queryIndex.
Definition Cigar.cpp:258

References getCigarCharOp(), and getExpandedCigarIndexFromQueryIndex().

◆ getCigarCharOpFromRefOffset()

char Cigar::getCigarCharOpFromRefOffset ( int32_t  refOffset)

Return the character code of the cigar operator associated with the specified reference offset.

'?' is returned for an out of range offset.

Definition at line 320 of file Cigar.cpp.

321{
323}
int32_t getExpandedCigarIndexFromRefOffset(int32_t refOffset)
Returns the index into the expanded cigar for the cigar associated with the specified reference offse...
Definition Cigar.cpp:273

References getCigarCharOp(), and getExpandedCigarIndexFromRefOffset().

◆ getCigarCharOpFromRefPos()

char Cigar::getCigarCharOpFromRefPos ( int32_t  refPosition,
int32_t  queryStartPos 
)

Return the character code of the cigar operator associated with the specified reference position.

'?' is returned for an out of range reference position.

Definition at line 326 of file Cigar.cpp.

327{
328 return(getCigarCharOp(getExpandedCigarIndexFromRefPos(refPosition, queryStartPos)));
329}
int32_t getExpandedCigarIndexFromRefPos(int32_t refPosition, int32_t queryStartPos)
Returns the index into the expanded cigar for the cigar associated with the specified reference posit...
Definition Cigar.cpp:288

References getCigarCharOp(), and getExpandedCigarIndexFromRefPos().

◆ getCigarString() [1/2]

void Cigar::getCigarString ( std::string &  cigarString) const

Set the passed in std::string to the string reprentation of the Cigar operations in this object.

Definition at line 36 of file Cigar.cpp.

37{
38 using namespace STLUtilities;
39
40 std::vector<CigarOperator>::const_iterator i;
41
42 cigarString.clear(); // clear result string
43
44 // Progressively append the character representations of the operations to
45 // the cigar string.
46 for (i = cigarOperations.begin(); i != cigarOperations.end(); i++)
47 {
48 cigarString << (*i).count << (*i).getChar();
49 }
50}
This file is inspired by the poor quality of string support in STL for what should be trivial capabil...

◆ getCigarString() [2/2]

void Cigar::getCigarString ( String cigarString) const

Set the passed in String to the string reprentation of the Cigar operations in this object.

Definition at line 52 of file Cigar.cpp.

53{
54 std::string cigar;
55
56 getCigarString(cigar);
57
58 cigarString = cigar.c_str();
59
60 return;
61}

References getCigarString().

Referenced by Dump(), getCigarString(), and SamRecord::setCigar().

◆ getExpandedCigarIndexFromQueryIndex()

int32_t Cigar::getExpandedCigarIndexFromQueryIndex ( int32_t  queryIndex)

Returns the index into the expanded cigar for the cigar associated with the specified queryIndex.

INDEX_NA returned if the index is out of range.

Definition at line 258 of file Cigar.cpp.

259{
260 // If the vectors aren't set, set them.
261 if ((queryToRef.size() == 0) || (refToQuery.size() == 0))
262 {
263 setQueryAndReferenceIndexes();
264 }
265 if ((queryIndex < 0) || ((uint32_t)queryIndex >= queryToCigar.size()))
266 {
267 return(INDEX_NA);
268 }
269 return(queryToCigar[queryIndex]);
270}
static const int32_t INDEX_NA
Value associated with an index that is not applicable/does not exist, used for converting between que...
Definition Cigar.h:492

References INDEX_NA.

Referenced by getCigarCharOpFromQueryIndex().

◆ getExpandedCigarIndexFromRefOffset()

int32_t Cigar::getExpandedCigarIndexFromRefOffset ( int32_t  refOffset)

Returns the index into the expanded cigar for the cigar associated with the specified reference offset.

INDEX_NA returned if the offset is out of range.

Definition at line 273 of file Cigar.cpp.

274{
275 // If the vectors aren't set, set them.
276 if ((queryToRef.size() == 0) || (refToQuery.size() == 0))
277 {
278 setQueryAndReferenceIndexes();
279 }
280 if ((refOffset < 0) || ((uint32_t)refOffset >= refToCigar.size()))
281 {
282 return(INDEX_NA);
283 }
284 return(refToCigar[refOffset]);
285}

References INDEX_NA.

Referenced by getCigarCharOpFromRefOffset(), and getExpandedCigarIndexFromRefPos().

◆ getExpandedCigarIndexFromRefPos()

int32_t Cigar::getExpandedCigarIndexFromRefPos ( int32_t  refPosition,
int32_t  queryStartPos 
)

Returns the index into the expanded cigar for the cigar associated with the specified reference position and queryStartPos.

INDEX_NA returned if the position is out of range.

Definition at line 288 of file Cigar.cpp.

290{
291 return(getExpandedCigarIndexFromRefOffset(refPosition - queryStartPos));
292}

References getExpandedCigarIndexFromRefOffset().

Referenced by getCigarCharOpFromRefPos().

◆ getExpandedString()

void Cigar::getExpandedString ( std::string &  s) const

Sets the specified string to a valid CIGAR string of characters that represent the cigar with no digits (a CIGAR of "3M" would return "MMM").

The returned string is actually also a valid CIGAR string. In theory this makes it easier to parse some reads.

Returns
s the string to populate

Definition at line 63 of file Cigar.cpp.

64{
65 s = "";
66
67 std::vector<CigarOperator>::const_iterator i;
68
69 // Progressively append the character representations of the operations to
70 // the string passed in
71
72 for (i = cigarOperations.begin(); i != cigarOperations.end(); i++)
73 {
74 for (uint32_t j = 0; j<(*i).count; j++) s += (*i).getChar();
75 }
76 return;
77}

◆ getExpectedQueryBaseCount()

int Cigar::getExpectedQueryBaseCount ( ) const

Return the length of the read that corresponds to the current CIGAR string.

For validation, we should expect that a sequence read in a SAM file will be the same length as the value returned by this method.

Example: 3M2D3M describes a read with three bases matching the reference, then skips 2 bases, then has three more bases that match the reference (match/mismatch). In this case, the read length is expected to be 6.

Example: 3M2I3M describes a read with 3 match/mismatch bases, two extra bases, and then 3 more match/mistmatch bases. The total in this example is 8 bases.

Returns
returns the expected read length

Definition at line 95 of file Cigar.cpp.

96{
97 int matchCount = 0;
98 std::vector<CigarOperator>::const_iterator i;
99 for (i = cigarOperations.begin(); i != cigarOperations.end(); i++)
100 {
101 switch (i->operation)
102 {
103 case match:
104 case mismatch:
105 case softClip:
106 case insert:
107 matchCount += i->count;
108 break;
109 default:
110 // we only care about operations that are in the query sequence.
111 break;
112 }
113 }
114 return matchCount;
115}

References insert, match, mismatch, and softClip.

Referenced by SamValidator::isValidCigar(), and SamFilter::softClip().

◆ getExpectedReferenceBaseCount()

int Cigar::getExpectedReferenceBaseCount ( ) const

Return the number of bases in the reference that this CIGAR "spans".

When doing range checking, we occassionally need to know how many total bases the CIGAR string represents as compared to the reference.

Examples: 3M2D3M describes a read that overlays 8 bases in the reference. 3M2I3M describes a read with 3 bases that match the reference, two additional bases that aren't in the reference, and 3 more bases that match the reference, so it spans 6 bases in the reference.

Returns
how many bases in the reference are spanned by the given CIGAR string

Definition at line 120 of file Cigar.cpp.

121{
122 int matchCount = 0;
123 std::vector<CigarOperator>::const_iterator i;
124 for (i = cigarOperations.begin(); i != cigarOperations.end(); i++)
125 {
126 switch (i->operation)
127 {
128 case match:
129 case mismatch:
130 case del:
131 case skip:
132 matchCount += i->count;
133 break;
134 default:
135 // we only care about operations that are in the reference sequence.
136 break;
137 }
138 }
139 return matchCount;
140}

References del, match, mismatch, and skip.

Referenced by SamTags::createMDTag().

◆ getNumBeginClips()

int Cigar::getNumBeginClips ( ) const

Return the number of clips that are at the beginning of the cigar.

Definition at line 144 of file Cigar.cpp.

145{
146 int numBeginClips = 0;
147 for (unsigned int i = 0; i != cigarOperations.size(); i++)
148 {
149 if ((cigarOperations[i].operation == softClip) ||
150 (cigarOperations[i].operation == hardClip))
151 {
152 // Clipping operator, increment the counter.
153 numBeginClips += cigarOperations[i].count;
154 }
155 else
156 {
157 // Break out of the loop since a non-clipping operator was found.
158 break;
159 }
160 }
161 return(numBeginClips);
162}

References hardClip, and softClip.

◆ getNumEndClips()

int Cigar::getNumEndClips ( ) const

Return the number of clips that are at the end of the cigar.

Definition at line 166 of file Cigar.cpp.

167{
168 int numEndClips = 0;
169 for (int i = (cigarOperations.size() - 1); i >= 0; i--)
170 {
171 if ((cigarOperations[i].operation == softClip) ||
172 (cigarOperations[i].operation == hardClip))
173 {
174 // Clipping operator, increment the counter.
175 numEndClips += cigarOperations[i].count;
176 }
177 else
178 {
179 // Break out of the loop since a non-clipping operator was found.
180 break;
181 }
182 }
183 return(numEndClips);
184}

References hardClip, and softClip.

◆ getNumOverlaps()

uint32_t Cigar::getNumOverlaps ( int32_t  start,
int32_t  end,
int32_t  queryStartPos 
)

Return the number of bases that overlap the reference and the read associated with this cigar that falls within the specified region.

Parameters
start: inclusive 0-based start position (reference position) of the region to check for overlaps in (-1 indicates to start at the beginning of the reference.)
end: exclusive 0-based end position (reference position) of the region to check for overlaps in (-1 indicates to go to the end of the reference.)
queryStartPos: 0-based leftmost mapping position of the first matcihng base in the query.

Definition at line 334 of file Cigar.cpp.

336{
337 // Get the overlap info.
338 if ((queryToRef.size() == 0) || (refToQuery.size() == 0))
339 {
340 setQueryAndReferenceIndexes();
341 }
342
343 // Get the start and end offsets.
344 int32_t startRefOffset = 0;
345 // If the specified start is more than the queryStartPos, set
346 // the startRefOffset to the appropriate non-zero value.
347 // (if start is <= queryStartPos, than startRefOffset is 0 - it should
348 // not be set to a negative value.)
349 if (start > queryStartPos)
350 {
351 startRefOffset = start - queryStartPos;
352 }
353
354 int32_t endRefOffset = end - queryStartPos;
355 if (end == -1)
356 {
357 // -1 means that the region goes to the end of the refrerence.
358 // So set endRefOffset to the max refOffset + 1 which is the
359 // size of the refToQuery vector.
360 endRefOffset = refToQuery.size();
361 }
362
363
364 // if endRefOffset is less than 0, then this read does not fall within
365 // the specified region, so return 0.
366 if (endRefOffset < 0)
367 {
368 return(0);
369 }
370
371 // Get the overlaps for these offsets.
372 // Loop through the read counting positions that match the reference
373 // within this region.
374 int32_t refOffset = 0;
375 int32_t numOverlaps = 0;
376 for (unsigned int queryIndex = 0; queryIndex < queryToRef.size();
377 queryIndex++)
378 {
379 refOffset = getRefOffset(queryIndex);
380 if (refOffset > endRefOffset)
381 {
382 // Past the end of the specified region, so stop checking
383 // for overlaps since there will be no more.
384 break;
385 }
386 else if ((refOffset >= startRefOffset) && (refOffset < endRefOffset))
387 {
388 // within the region, increment the counter.
389 ++numOverlaps;
390 }
391 }
392
393 return(numOverlaps);
394}
int32_t getRefOffset(int32_t queryIndex)
Return the reference offset associated with the specified query index or INDEX_NA based on this cigar...
Definition Cigar.cpp:187

References getRefOffset().

Referenced by SamRecord::getNumOverlaps().

◆ getOperator()

const CigarOperator & Cigar::getOperator ( int  i) const
inline

Return the Cigar Operation at the specified index (starting at 0).

Definition at line 354 of file Cigar.h.

355 {
356 return cigarOperations[i];
357 }

Referenced by SamFilter::softClip(), CigarHelper::softClipBeginByRefPos(), and CigarHelper::softClipEndByRefPos().

◆ getQueryIndex() [1/2]

int32_t Cigar::getQueryIndex ( int32_t  refOffset)

Return the query index associated with the specified reference offset or INDEX_NA based on this cigar.

Definition at line 202 of file Cigar.cpp.

203{
204 // If the vectors aren't set, set them.
205 if ((queryToRef.size() == 0) || (refToQuery.size() == 0))
206 {
207 setQueryAndReferenceIndexes();
208 }
209 if ((refOffset < 0) || ((uint32_t)refOffset >= refToQuery.size()))
210 {
211 return(INDEX_NA);
212 }
213 return(refToQuery[refOffset]);
214}

References INDEX_NA.

Referenced by PileupElementBaseQual::addEntry(), SamRecordHelper::checkSequence(), and SamTags::createMDTag().

◆ getQueryIndex() [2/2]

int32_t Cigar::getQueryIndex ( int32_t  refPosition,
int32_t  queryStartPos 
)

Return the query index or INDEX_NA associated with the specified reference offset when the query starts at the specified reference position.

Definition at line 240 of file Cigar.cpp.

241{
242 // If the vectors aren't set, set them.
243 if ((queryToRef.size() == 0) || (refToQuery.size() == 0))
244 {
245 setQueryAndReferenceIndexes();
246 }
247
248 int32_t refOffset = refPosition - queryStartPos;
249 if ((refOffset < 0) || ((uint32_t)refOffset >= refToQuery.size()))
250 {
251 return(INDEX_NA);
252 }
253
254 return(refToQuery[refOffset]);
255}

References INDEX_NA.

◆ getRefOffset()

int32_t Cigar::getRefOffset ( int32_t  queryIndex)

Return the reference offset associated with the specified query index or INDEX_NA based on this cigar.

Definition at line 187 of file Cigar.cpp.

188{
189 // If the vectors aren't set, set them.
190 if ((queryToRef.size() == 0) || (refToQuery.size() == 0))
191 {
192 setQueryAndReferenceIndexes();
193 }
194 if ((queryIndex < 0) || ((uint32_t)queryIndex >= queryToRef.size()))
195 {
196 return(INDEX_NA);
197 }
198 return(queryToRef[queryIndex]);
199}

References INDEX_NA.

Referenced by SamQuerySeqWithRefIter::getNextMatchMismatch(), getNumOverlaps(), SamQuerySeqWithRef::seqWithEquals(), and SamQuerySeqWithRef::seqWithoutEquals().

◆ getRefPosition()

int32_t Cigar::getRefPosition ( int32_t  queryIndex,
int32_t  queryStartPos 
)

Return the reference position associated with the specified query index or INDEX_NA based on this cigar and the specified queryStartPos which is the leftmost mapping position of the first matching base in the query.

Definition at line 217 of file Cigar.cpp.

218{
219 // If the vectors aren't set, set them.
220 if ((queryToRef.size() == 0) || (refToQuery.size() == 0))
221 {
222 setQueryAndReferenceIndexes();
223 }
224 if ((queryIndex < 0) || ((uint32_t)queryIndex >= queryToRef.size()))
225 {
226 return(INDEX_NA);
227 }
228
229 if (queryToRef[queryIndex] != INDEX_NA)
230 {
231 return(queryToRef[queryIndex] + queryStartPos);
232 }
233 return(INDEX_NA);
234}

References INDEX_NA.

Referenced by SamFilter::softClip().

◆ hasIndel()

bool Cigar::hasIndel ( )

Return whether or not the cigar has indels (insertions or delections)

Returns
true if it has an insertion or deletion, false if not.

Definition at line 398 of file Cigar.cpp.

399{
400 for(unsigned int i = 0; i < cigarOperations.size(); i++)
401 {
402 if((cigarOperations[i].operation == insert) ||
403 (cigarOperations[i].operation == del))
404 {
405 // Found an indel, so return true.
406 return(true);
407 }
408 }
409 // Went through all the operations, and found no indel, so return false.
410 return(false);
411}

References del, and insert.

◆ isClip() [1/3]

static bool Cigar::isClip ( char  op)
inlinestatic

Return true if the specified operation is a clipping operation, false if not.

Definition at line 276 of file Cigar.h.

277 {
278 switch(op)
279 {
280 case 'S':
281 case 'H':
282 return true;
283 default:
284 return false;
285 }
286 return false;
287 }

◆ isClip() [2/3]

static bool Cigar::isClip ( const CigarOperator op)
inlinestatic

Return true if the specified operation is a clipping operation, false if not.

Definition at line 291 of file Cigar.h.

292 {
293 return(isClip(op.operation));
294 }
static bool isClip(Operation op)
Return true if the specified operation is a clipping operation, false if not.
Definition Cigar.h:261

References isClip().

◆ isClip() [3/3]

static bool Cigar::isClip ( Operation  op)
inlinestatic

Return true if the specified operation is a clipping operation, false if not.

Definition at line 261 of file Cigar.h.

262 {
263 switch(op)
264 {
265 case softClip:
266 case hardClip:
267 return true;
268 default:
269 return false;
270 }
271 return false;
272 }

References hardClip, and softClip.

Referenced by isClip(), SamFilter::softClip(), and CigarHelper::softClipEndByRefPos().

◆ isMatchOrMismatch() [1/2]

static bool Cigar::isMatchOrMismatch ( const CigarOperator op)
inlinestatic

Return true if the specified operation is a match/mismatch operation, false if not.

Definition at line 313 of file Cigar.h.

314 {
315 return(isMatchOrMismatch(op.operation));
316 }
static bool isMatchOrMismatch(Operation op)
Return true if the specified operation is a match/mismatch operation, false if not.
Definition Cigar.h:298

References isMatchOrMismatch().

◆ isMatchOrMismatch() [2/2]

static bool Cigar::isMatchOrMismatch ( Operation  op)
inlinestatic

Return true if the specified operation is a match/mismatch operation, false if not.

Definition at line 298 of file Cigar.h.

299 {
300 switch(op)
301 {
302 case match:
303 case mismatch:
304 return true;
305 default:
306 return false;
307 }
308 return false;
309 }

References match, and mismatch.

Referenced by isMatchOrMismatch(), and SamRecord::shiftIndelsLeft().

◆ operator==()

bool Cigar::operator== ( Cigar rhs) const

Return true if the 2 Cigars are the same (the same operations of the same sizes).

Definition at line 80 of file Cigar.cpp.

81{
82
83 if (this->size() != rhs.size()) return false;
84
85 for (int i = 0; i < this->size(); i++)
86 {
87 if (cigarOperations[i]!=rhs.cigarOperations[i]) return false;
88 }
89 return true;
90}
int size() const
Return the number of cigar operations.
Definition Cigar.h:364

References size().

◆ operator[]()

const CigarOperator & Cigar::operator[] ( int  i) const
inline

Return the Cigar Operation at the specified index (starting at 0).

Definition at line 348 of file Cigar.h.

349 {
350 return cigarOperations[i];
351 }

◆ setQueryAndReferenceIndexes()

void Cigar::setQueryAndReferenceIndexes ( )
protected

Definition at line 441 of file Cigar.cpp.

442{
443 // First ensure that the vectors are clear by clearing them.
444 clearQueryAndReferenceIndexes();
445
446 int extPos = 0;
447
448 // Process each cigar index.
449 for (uint32_t cigarIndex = 0; cigarIndex < cigarOperations.size(); cigarIndex++)
450 {
451 // Process the cigar operation.
452 switch (cigarOperations[cigarIndex].operation)
453 {
454 case match:
455 case mismatch:
456 // For match/mismatch, update the maps between query
457 // and reference for the number of matches/mismatches.
458 for (uint32_t i = 0; i < cigarOperations[cigarIndex].count; i++)
459 {
460 // The associated indexes are the next location in
461 // each array, which is equal to the current size.
462 int32_t queryToRefLen = queryToRef.size();
463 int32_t refToQueryLen = refToQuery.size();
464 queryToRef.push_back(refToQueryLen);
465 refToQuery.push_back(queryToRefLen);
466 refToCigar.push_back(extPos);
467 queryToCigar.push_back(extPos++);
468 myExpandedCigar.push_back(cigarOperations[cigarIndex].getChar());
469 }
470 break;
471 case insert:
472 case softClip:
473 // Add N/A reference offset for each query index that this
474 // insert covers.
475 for (uint32_t i = 0; i < cigarOperations[cigarIndex].count; i++)
476 {
477 queryToRef.push_back(INDEX_NA);
478 queryToCigar.push_back(extPos++);
479 myExpandedCigar.push_back(cigarOperations[cigarIndex].getChar());
480 }
481 break;
482 case del:
483 case skip:
484 // Add N/A query index for each reference offset that this
485 // deletion/skip covers.
486 for (uint32_t i = 0; i < cigarOperations[cigarIndex].count; i++)
487 {
488 refToQuery.push_back(INDEX_NA);
489 refToCigar.push_back(extPos++);
490 myExpandedCigar.push_back(cigarOperations[cigarIndex].getChar());
491 }
492 break;
493 case hardClip:
494 case pad:
495 case none:
496 for (uint32_t i = 0; i < cigarOperations[cigarIndex].count; i++)
497 {
498 myExpandedCigar.push_back(cigarOperations[cigarIndex].getChar());
499 ++extPos;
500 }
501 break;
502 };
503 }
504}

◆ size()

int Cigar::size ( ) const
inline

Return the number of cigar operations.

Definition at line 364 of file Cigar.h.

365 {
366 return cigarOperations.size();
367 }

Referenced by operator==(), SamRecord::shiftIndelsLeft(), SamFilter::softClip(), CigarHelper::softClipBeginByRefPos(), and CigarHelper::softClipEndByRefPos().

Friends And Related Symbol Documentation

◆ operator<<

std::ostream & operator<< ( std::ostream &  stream,
const Cigar cigar 
)
friend

Writes all of the cigar operations contained in the cigar to the passed in stream.

Definition at line 540 of file Cigar.h.

541{
542 stream << cigar.cigarOperations;
543 return stream;
544}

Member Data Documentation

◆ cigarOperations

std::vector<CigarOperator> Cigar::cigarOperations
protected

Definition at line 502 of file Cigar.h.

◆ INDEX_NA

const int32_t Cigar::INDEX_NA = -1
static

Value associated with an index that is not applicable/does not exist, used for converting between query and reference indexes/offsets when an associated index/offset does not exist.

Definition at line 492 of file Cigar.h.

Referenced by PileupElementBaseQual::addEntry(), SamRecordHelper::checkSequence(), SamTags::createMDTag(), getExpandedCigarIndexFromQueryIndex(), getExpandedCigarIndexFromRefOffset(), SamQuerySeqWithRefIter::getNextMatchMismatch(), getQueryIndex(), getQueryIndex(), getRefOffset(), getRefPosition(), SamQuerySeqWithRef::seqWithEquals(), SamQuerySeqWithRef::seqWithoutEquals(), and SamFilter::softClip().

◆ MAX_OP_VALUE

const int Cigar::MAX_OP_VALUE = pad
static

Definition at line 101 of file Cigar.h.


The documentation for this class was generated from the following files: