libStatGen Software  1
SamFilter Class Reference

Class for helping to filter a SAM/BAM record. More...

#include <SamFilter.h>

Public Types

enum  FilterStatus { NONE, CLIPPED, FILTERED }
 Enum describing what sort of filtering was done. More...
 

Static Public Member Functions

static FilterStatus clipOnMismatchThreshold (SamRecord &record, GenomeSequence &refSequence, double mismatchThreshold)
 Clip the read based on the specified mismatch threshold. More...
 
static FilterStatus softClip (SamRecord &record, int32_t numFrontClips, int32_t numBackClips)
 Soft clip the record from the front and/or the back. More...
 
static FilterStatus softClip (Cigar &oldCigar, int32_t numFrontClips, int32_t numBackClips, int32_t &startPos, CigarRoller &updatedCigar)
 Soft clip the cigar from the front and/or the back, writing the value into the new cigar, updatedCigar & startPos are only updated if the return FilterStatus is CLIPPED. More...
 
static FilterStatus filterOnMismatchQuality (SamRecord &record, GenomeSequence &refSequence, uint32_t qualityThreshold, uint8_t defaultQualityInt)
 Filter the read based on the specified quality threshold. More...
 
static uint32_t sumMismatchQuality (SamRecord &record, GenomeSequence &refSequence, uint8_t defaultQualityInt)
 Get the sum of the qualities of all mismatches in the record. More...
 
static void filterRead (SamRecord &record)
 Filter the read by marking it as unmapped.
 

Detailed Description

Class for helping to filter a SAM/BAM record.

Definition at line 25 of file SamFilter.h.

Member Enumeration Documentation

◆ FilterStatus

Enum describing what sort of filtering was done.

Enumerator
NONE 

The filter did not affect the read.

CLIPPED 

Filtering clipped the read.

FILTERED 

Filtering caused the read to be modified to unmapped.

Definition at line 29 of file SamFilter.h.

29  {
30  NONE, ///< The filter did not affect the read.
31  CLIPPED, ///< Filtering clipped the read.
32  FILTERED ///< Filtering caused the read to be modified to unmapped.
33  };
Filtering clipped the read.
Definition: SamFilter.h:31
The filter did not affect the read.
Definition: SamFilter.h:30
Filtering caused the read to be modified to unmapped.
Definition: SamFilter.h:32

Member Function Documentation

◆ clipOnMismatchThreshold()

SamFilter::FilterStatus SamFilter::clipOnMismatchThreshold ( SamRecord record,
GenomeSequence refSequence,
double  mismatchThreshold 
)
static

Clip the read based on the specified mismatch threshold.

Returns
how the read was affected, NONE if the read was not modified, CLIPPED if the read was clipped, FILTERED if the whole read would have been clipped so instead the read was modified to unmapped.

Definition at line 27 of file SamFilter.cpp.

References SamQuerySeqWithRefIter::getNextMatchMismatch(), SamSingleBaseMatchInfo::getQueryIndex(), SamRecord::getReadLength(), SamSingleBaseMatchInfo::getType(), and softClip().

30 {
31  // Read & clip from the left & right.
32  SamQuerySeqWithRefIter iterFromFront(record, refSequence, true);
33  SamQuerySeqWithRefIter iterFromBack(record, refSequence, false);
34 
35  SamSingleBaseMatchInfo baseMatchInfo;
36 
37  int32_t readLength = record.getReadLength();
38  // Init last front clip to be prior to the lastFront index (0).
39  const int32_t initialLastFrontClipPos = -1;
40  int32_t lastFrontClipPos = initialLastFrontClipPos;
41  // Init first back clip to be past the last index (readLength).
42  int32_t firstBackClipPos = readLength;
43 
44  bool fromFrontComplete = false;
45  bool fromBackComplete = false;
46  int32_t numBasesFromFront = 0;
47  int32_t numBasesFromBack = 0;
48  int32_t numMismatchFromFront = 0;
49  int32_t numMismatchFromBack = 0;
50 
51  //////////////////////////////////////////////////////////
52  // Determining the clip positions.
53  while(!fromFrontComplete || !fromBackComplete)
54  {
55  // Read from the front (left to right) of the read until
56  // more have been read from that direction than the opposite direction.
57  while(!fromFrontComplete &&
58  ((numBasesFromFront <= numBasesFromBack) ||
59  (fromBackComplete)))
60  {
61  if(iterFromFront.getNextMatchMismatch(baseMatchInfo) == false)
62  {
63  // Nothing more to read in this direction.
64  fromFrontComplete = true;
65  break;
66  }
67  // Got a read. Check to see if it is to or past the last clip.
68  if(baseMatchInfo.getQueryIndex() >= firstBackClipPos)
69  {
70  // This base is past where we are clipping, so we
71  // are done reading in this direction.
72  fromFrontComplete = true;
73  break;
74  }
75  // This is an actual base read from the left to the
76  // right, so up the counter and determine if it was a mismatch.
77  ++numBasesFromFront;
78 
79  if(baseMatchInfo.getType() == SamSingleBaseMatchInfo::MISMATCH)
80  {
81  // Mismatch
82  ++numMismatchFromFront;
83  // Check to see if it is over the threshold.
84  double mismatchPercent =
85  (double)numMismatchFromFront / numBasesFromFront;
86  if(mismatchPercent > mismatchThreshold)
87  {
88  // Need to clip.
89  lastFrontClipPos = baseMatchInfo.getQueryIndex();
90  // Reset the counters.
91  numBasesFromFront = 0;
92  numMismatchFromFront = 0;
93  }
94  }
95  }
96 
97  // Now, read from right to left until more have been read
98  // from the back than from the front.
99  while(!fromBackComplete &&
100  ((numBasesFromBack <= numBasesFromFront) ||
101  (fromFrontComplete)))
102  {
103  if(iterFromBack.getNextMatchMismatch(baseMatchInfo) == false)
104  {
105  // Nothing more to read in this direction.
106  fromBackComplete = true;
107  break;
108  }
109  // Got a read. Check to see if it is to or past the first clip.
110  if(baseMatchInfo.getQueryIndex() <= lastFrontClipPos)
111  {
112  // This base is past where we are clipping, so we
113  // are done reading in this direction.
114  fromBackComplete = true;
115  break;
116  }
117  // This is an actual base read from the right to the
118  // left, so up the counter and determine if it was a mismatch.
119  ++numBasesFromBack;
120 
121  if(baseMatchInfo.getType() == SamSingleBaseMatchInfo::MISMATCH)
122  {
123  // Mismatch
124  ++numMismatchFromBack;
125  // Check to see if it is over the threshold.
126  double mismatchPercent =
127  (double)numMismatchFromBack / numBasesFromBack;
128  if(mismatchPercent > mismatchThreshold)
129  {
130  // Need to clip.
131  firstBackClipPos = baseMatchInfo.getQueryIndex();
132  // Reset the counters.
133  numBasesFromBack = 0;
134  numMismatchFromBack = 0;
135  }
136  }
137  }
138  }
139 
140  //////////////////////////////////////////////////////////
141  // Done determining the clip positions, so clip.
142  // To determine the number of clips from the front, add 1 to the
143  // lastFrontClipPos since the index starts at 0.
144  // To determine the number of clips from the back, subtract the
145  // firstBackClipPos from the readLength.
146  // Example:
147  // Pos: 012345
148  // Read: AAAAAA
149  // Read Length = 6. If lastFrontClipPos = 2 and firstBackClipPos = 4, numFrontClips = 3 & numBack = 2.
150  return(softClip(record, lastFrontClipPos + 1, readLength - firstBackClipPos));
151 }
Type getType()
Get the type (match/mismatch/unknown) for this object.
int32_t getReadLength()
Get the length of the read.
Definition: SamRecord.cpp:1379
Iterates through the query and compare with reference.
int32_t getQueryIndex()
Get the query index for this object.
static FilterStatus softClip(SamRecord &record, int32_t numFrontClips, int32_t numBackClips)
Soft clip the record from the front and/or the back.
Definition: SamFilter.cpp:155
This class contains the match/mismatch information between the reference and a read for a single base...

◆ filterOnMismatchQuality()

SamFilter::FilterStatus SamFilter::filterOnMismatchQuality ( SamRecord record,
GenomeSequence refSequence,
uint32_t  qualityThreshold,
uint8_t  defaultQualityInt 
)
static

Filter the read based on the specified quality threshold.

Returns
how the read was affected, NONE if the read was not modified, FILTERED if the read was modified to unmapped because it was over the quality threshold.

Definition at line 430 of file SamFilter.cpp.

References FILTERED, filterRead(), NONE, and sumMismatchQuality().

434 {
435  uint32_t totalMismatchQuality =
436  sumMismatchQuality(record, refSequence, defaultQualityInt);
437 
438  // If the total mismatch quality is over the threshold,
439  // filter the read.
440  if(totalMismatchQuality > qualityThreshold)
441  {
442  filterRead(record);
443  return(FILTERED);
444  }
445  return(NONE);
446 }
static uint32_t sumMismatchQuality(SamRecord &record, GenomeSequence &refSequence, uint8_t defaultQualityInt)
Get the sum of the qualities of all mismatches in the record.
Definition: SamFilter.cpp:451
The filter did not affect the read.
Definition: SamFilter.h:30
static void filterRead(SamRecord &record)
Filter the read by marking it as unmapped.
Definition: SamFilter.cpp:486
Filtering caused the read to be modified to unmapped.
Definition: SamFilter.h:32

◆ softClip() [1/2]

SamFilter::FilterStatus SamFilter::softClip ( SamRecord record,
int32_t  numFrontClips,
int32_t  numBackClips 
)
static

Soft clip the record from the front and/or the back.

Parameters
recordrecord to be clipped (input/output parameter).
numFrontClipsnumber of bases that should be clipped from the front of the sequence read. (total count, including any that are already clipped.)
backClipPosnumber of bases that should be clipped from the back of the sequence read. (total count, including any that are already clipped.)

Definition at line 155 of file SamFilter.cpp.

References CLIPPED, FILTERED, filterRead(), SamRecord::get0BasedPosition(), SamRecord::getCigarInfo(), NONE, SamRecord::set0BasedPosition(), and SamRecord::setCigar().

Referenced by clipOnMismatchThreshold().

158 {
159  //////////////////////////////////////////////////////////
160  Cigar* cigar = record.getCigarInfo();
161  FilterStatus status = NONE;
162  int32_t startPos = record.get0BasedPosition();
163  CigarRoller updatedCigar;
164 
165  status = softClip(*cigar, numFrontClips, numBackClips,
166  startPos, updatedCigar);
167 
168  if(status == FILTERED)
169  {
170  /////////////////////////////
171  // The entire read is clipped, so rather than clipping it,
172  // filter it out.
173  filterRead(record);
174  return(FILTERED);
175  }
176  else if(status == CLIPPED)
177  {
178  // Part of the read was clipped, and now that we have
179  // an updated cigar, update the read.
180  record.setCigar(updatedCigar);
181 
182  // Update the starting position.
183  record.set0BasedPosition(startPos);
184  }
185  return(status);
186 }
Filtering clipped the read.
Definition: SamFilter.h:31
The filter did not affect the read.
Definition: SamFilter.h:30
Cigar * getCigarInfo()
Returns a pointer to the Cigar object associated with this record.
Definition: SamRecord.cpp:1824
This class represents the CIGAR without any methods to set the cigar (see CigarRoller for that)...
Definition: Cigar.h:83
static void filterRead(SamRecord &record)
Filter the read by marking it as unmapped.
Definition: SamFilter.cpp:486
Filtering caused the read to be modified to unmapped.
Definition: SamFilter.h:32
bool setCigar(const char *cigar)
Set the CIGAR to the specified SAM formatted cigar string.
Definition: SamRecord.cpp:259
FilterStatus
Enum describing what sort of filtering was done.
Definition: SamFilter.h:29
bool set0BasedPosition(int32_t position)
Set the leftmost position using the specified 0-based (BAM format) value.
Definition: SamRecord.cpp:242
static FilterStatus softClip(SamRecord &record, int32_t numFrontClips, int32_t numBackClips)
Soft clip the record from the front and/or the back.
Definition: SamFilter.cpp:155
The purpose of this class is to provide accessors for setting, updating, modifying the CIGAR object...
Definition: CigarRoller.h:66
int32_t get0BasedPosition()
Get the 0-based(BAM) leftmost position of the record.
Definition: SamRecord.cpp:1307

◆ softClip() [2/2]

SamFilter::FilterStatus SamFilter::softClip ( Cigar oldCigar,
int32_t  numFrontClips,
int32_t  numBackClips,
int32_t &  startPos,
CigarRoller updatedCigar 
)
static

Soft clip the cigar from the front and/or the back, writing the value into the new cigar, updatedCigar & startPos are only updated if the return FilterStatus is CLIPPED.

Parameters
oldCigarcigar prior to clipping
numFrontClipsnumber of bases that should be clipped from the front of the sequence read. (total count, including any that are already clipped.)
numBackClipsnumber of bases that should be clipped from the back of the sequence read. (total count, including any that are already clipped.)
startPos0-based start position associated with the cigar prior to updating (input) and set to the 0-based start position after updating (output) the cigar if it was CLIPPED.
updatedCigarset to the clipped cigar if CLIPPED (output param).

Definition at line 191 of file SamFilter.cpp.

References CigarRoller::Add(), CLIPPED, Cigar::del, FILTERED, Cigar::foundInQuery(), Cigar::getExpectedQueryBaseCount(), Cigar::getOperator(), Cigar::getRefPosition(), Cigar::hardClip, Cigar::INDEX_NA, Cigar::insert, Cigar::isClip(), Cigar::match, Cigar::mismatch, NONE, Cigar::none, Cigar::size(), Cigar::skip, and Cigar::softClip.

196 {
197  int32_t readLength = oldCigar.getExpectedQueryBaseCount();
198  int32_t endClipPos = readLength - numBackClips;
199  FilterStatus status = NONE;
200 
201  if((numFrontClips != 0) || (numBackClips != 0))
202  {
203  // Clipping from front and/or from the back.
204 
205  // Check to see if the entire read was clipped.
206  int32_t totalClips = numFrontClips + numBackClips;
207  if(totalClips >= readLength)
208  {
209  /////////////////////////////
210  // The entire read is clipped, so rather than clipping it,
211  // filter it out.
212  return(FILTERED);
213  }
214 
215  // Part of the read was clipped.
216  status = CLIPPED;
217 
218  // Loop through, creating an updated cigar.
219  int origCigarOpIndex = 0;
220 
221  // Track how many read positions are covered up to this
222  // point by the cigar to determine up to up to what
223  // point in the cigar is affected by this clipping.
224  int32_t numPositions = 0;
225 
226  // Track if any non-clips are in the new cigar.
227  bool onlyClips = true;
228 
229  const Cigar::CigarOperator* op = NULL;
230 
231  //////////////////
232  // Clip from front
233  while((origCigarOpIndex < oldCigar.size()) &&
234  (numPositions < numFrontClips))
235  {
236  op = &(oldCigar.getOperator(origCigarOpIndex));
237  switch(op->operation)
238  {
239  case Cigar::hardClip:
240  // Keep this operation as the new clips do not
241  // affect other clips.
242  updatedCigar += *op;
243  break;
244  case Cigar::del:
245  case Cigar::skip:
246  // Skip and delete are going to be dropped, and
247  // are not in the read, so the read index doesn't
248  // need to be updated
249  break;
250  case Cigar::insert:
251  case Cigar::match:
252  case Cigar::mismatch:
253  case Cigar::softClip:
254  // Update the read index as these types
255  // are found in the read.
256  numPositions += op->count;
257  break;
258  case Cigar::none:
259  default:
260  // Nothing to do for none.
261  break;
262  };
263  ++origCigarOpIndex;
264  }
265 
266  // If bases were clipped from the front, add the clip and
267  // any partial cigar operation as necessary.
268  if(numFrontClips != 0)
269  {
270  // Add the softclip to the front of the read.
271  updatedCigar.Add(Cigar::softClip, numFrontClips);
272 
273  // Add the rest of the last Cigar operation if
274  // it is not entirely clipped.
275  int32_t newCount = numPositions - numFrontClips;
276  if(newCount > 0)
277  {
278  // Before adding it, check to see if the same
279  // operation is clipped from the end.
280  // numPositions greater than the endClipPos
281  // means that it is equal or past that position,
282  // so shorten the number of positions.
283  if(numPositions > endClipPos)
284  {
285  newCount -= (numPositions - endClipPos);
286  }
287  if(newCount > 0)
288  {
289  updatedCigar.Add(op->operation, newCount);
290  if(!Cigar::isClip(op->operation))
291  {
292  onlyClips = false;
293  }
294  }
295  }
296  }
297 
298  // Add operations until the point of the end clip is reached.
299  // For example...
300  // 2M1D3M = MMDMMM readLength = 5
301  // readIndex: 01 234
302  // at cigarOpIndex 0 (2M), numPositions = 2.
303  // at cigarOpIndex 1 (1D), numPositions = 2.
304  // at cigarOpIndex 2 (3M), numPositions = 5.
305  // if endClipPos = 2, we still want to consume the 1D, so
306  // need to keep looping until numPositions > endClipPos
307  while((origCigarOpIndex < oldCigar.size()) &&
308  (numPositions <= endClipPos))
309  {
310  op = &(oldCigar.getOperator(origCigarOpIndex));
311 
312  // Update the numPositions count if the operations indicates
313  // bases within the read.
314  if(!Cigar::foundInQuery(op->operation))
315  {
316  // This operation is not in the query read sequence,
317  // so it is not yet to the endClipPos, just add the
318  // operation do not increment the number of positions.
319  updatedCigar += *op;
320  if(!Cigar::isClip(op->operation))
321  {
322  onlyClips = false;
323  }
324  }
325  else
326  {
327  // This operation appears in the query sequence, so
328  // check to see if the clip occurs in this operation.
329 
330  // endClipPos is 0 based & numPositions is a count.
331  // If endClipPos is 4, then it is the 5th position.
332  // If 4 positions are covered so far (numPositions = 4),
333  // then we are right at endCLipPos: 4-4 = 0, none of
334  // this operation should be kept.
335  // If only 3 positions were covered, then we are at offset
336  // 3, so offset 3 should be added: 4-3 = 1.
337  uint32_t numPosTilClip = endClipPos - numPositions;
338 
339  if(numPosTilClip < op->count)
340  {
341  // this operation is partially clipped, write the part
342  // that was not clipped if it is not all clipped.
343  if(numPosTilClip != 0)
344  {
345  updatedCigar.Add(op->operation,
346  numPosTilClip);
347  if(!Cigar::isClip(op->operation))
348  {
349  onlyClips = false;
350  }
351  }
352  }
353  else
354  {
355  // This operation is not clipped, so add it
356  updatedCigar += *op;
357  if(!Cigar::isClip(op->operation))
358  {
359  onlyClips = false;
360  }
361  }
362  // This operation occurs in the query sequence, so
363  // increment the number of positions covered.
364  numPositions += op->count;
365  }
366 
367  // Move to the next cigar position.
368  ++origCigarOpIndex;
369  }
370 
371  //////////////////
372  // Add the softclip to the back.
373  if(numBackClips != 0)
374  {
375  // Add the softclip to the end
376  updatedCigar.Add(Cigar::softClip, numBackClips);
377  }
378 
379  //////////////////
380  // Add any hardclips remaining in the original cigar to the back.
381  while(origCigarOpIndex < oldCigar.size())
382  {
383  op = &(oldCigar.getOperator(origCigarOpIndex));
384  if(op->operation == Cigar::hardClip)
385  {
386  // Keep this operation as the new clips do not
387  // affect other clips.
388  updatedCigar += *op;
389  }
390  ++origCigarOpIndex;
391  }
392 
393  // Check to see if the new cigar is only clips.
394  if(onlyClips)
395  {
396  // Only clips in the new cigar, so mark the read as filtered
397  // instead of updating the cigar.
398  /////////////////////////////
399  // The entire read was clipped.
400  status = FILTERED;
401  }
402  else
403  {
404  // Part of the read was clipped.
405  // Update the starting position if a clip was added to
406  // the front.
407  if(numFrontClips > 0)
408  {
409  // Convert from query index to reference position (from the
410  // old cigar)
411  // Get the position for the last front clipped position by
412  // getting the position associated with the clipped base on
413  // the reference. Then add one to get to the first
414  // non-clipped position.
415  int32_t lastFrontClipPos = numFrontClips - 1;
416  int32_t newStartPos = oldCigar.getRefPosition(lastFrontClipPos,
417  startPos);
418  if(newStartPos != Cigar::INDEX_NA)
419  {
420  // Add one to get first non-clipped position.
421  startPos = newStartPos + 1;
422  }
423  }
424  }
425  }
426  return(status);
427 }
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 cig...
Definition: Cigar.cpp:217
insertion to the reference (the query sequence contains bases that have no corresponding base in the ...
Definition: Cigar.h:91
static bool isClip(Operation op)
Return true if the specified operation is a clipping operation, false if not.
Definition: Cigar.h:261
void Add(Operation operation, int count)
Append the specified operation with the specified count to this object.
Definition: CigarRoller.cpp:77
Filtering clipped the read.
Definition: SamFilter.h:31
skipped region from the reference (the reference contains bases that have no corresponding base in th...
Definition: Cigar.h:93
no operation has been set.
Definition: Cigar.h:88
The filter did not affect the read.
Definition: SamFilter.h:30
int size() const
Return the number of cigar operations.
Definition: Cigar.h:364
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
Hard clip on the read (clipped sequence not present in the query sequence or reference). Associated with CIGAR Operation "H".
Definition: Cigar.h:95
static bool foundInQuery(Operation op)
Return true if the specified operation is found in the query sequence, false if not.
Definition: Cigar.h:219
mismatch operation. Associated with CIGAR Operation "M"
Definition: Cigar.h:90
Filtering caused the read to be modified to unmapped.
Definition: SamFilter.h:32
Soft clip on the read (clipped sequence present in the query sequence, but not in reference)...
Definition: Cigar.h:94
match/mismatch operation. Associated with CIGAR Operation "M"
Definition: Cigar.h:89
deletion from the reference (the reference contains bases that have no corresponding base in the quer...
Definition: Cigar.h:92
int getExpectedQueryBaseCount() const
Return the length of the read that corresponds to the current CIGAR string.
Definition: Cigar.cpp:95
FilterStatus
Enum describing what sort of filtering was done.
Definition: SamFilter.h:29
const CigarOperator & getOperator(int i) const
Return the Cigar Operation at the specified index (starting at 0).
Definition: Cigar.h:354

◆ sumMismatchQuality()

uint32_t SamFilter::sumMismatchQuality ( SamRecord record,
GenomeSequence refSequence,
uint8_t  defaultQualityInt 
)
static

Get the sum of the qualities of all mismatches in the record.

Parameters
recordrecord on which to calculate the sum the mismatch qualities
refSequencereference to use to check for mismatches.
defaultQualityIntdefault value to use for the quality if no quality was specified in the read.
Returns
sum of the qualities of mismatches

Definition at line 451 of file SamFilter.cpp.

References SamQuerySeqWithRefIter::getNextMatchMismatch(), BaseUtilities::getPhredBaseQuality(), SamRecord::getQuality(), SamSingleBaseMatchInfo::getQueryIndex(), SamSingleBaseMatchInfo::getType(), and BaseUtilities::UNKNOWN_QUALITY_INT.

Referenced by filterOnMismatchQuality().

454 {
455  // Track the mismatch info.
456  int mismatchQual = 0;
457  int numMismatch = 0;
458 
459  SamQuerySeqWithRefIter sequenceIter(record, refSequence);
460 
461  SamSingleBaseMatchInfo baseMatchInfo;
462  while(sequenceIter.getNextMatchMismatch(baseMatchInfo))
463  {
464  if(baseMatchInfo.getType() == SamSingleBaseMatchInfo::MISMATCH)
465  {
466  // Got a mismatch, get the associated quality.
467  char readQualityChar =
468  record.getQuality(baseMatchInfo.getQueryIndex());
469  uint8_t readQualityInt =
470  BaseUtilities::getPhredBaseQuality(readQualityChar);
471 
472  if(readQualityInt == BaseUtilities::UNKNOWN_QUALITY_INT)
473  {
474  // Quality was not specified, so use the configured setting.
475  readQualityInt = defaultQualityInt;
476  }
477  mismatchQual += readQualityInt;
478  ++numMismatch;
479  }
480  }
481 
482  return(mismatchQual);
483 }
Type getType()
Get the type (match/mismatch/unknown) for this object.
Iterates through the query and compare with reference.
const char * getQuality()
Returns the SAM formatted quality string (QUAL).
Definition: SamRecord.cpp:1626
static uint8_t getPhredBaseQuality(char charQuality)
Get phred base quality from the specified ascii quality.
int32_t getQueryIndex()
Get the query index for this object.
static const uint8_t UNKNOWN_QUALITY_INT
Int value used when the quality is unknown.
Definition: BaseUtilities.h:51
This class contains the match/mismatch information between the reference and a read for a single base...

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