18 #include "TestEquals.h"
19 #include "SamQuerySeqWithRefHelper.h"
28 EqualsTest::testEq(EqualsTest::SAM);
29 #ifdef __ZLIB_AVAILABLE__
30 EqualsTest::testEq(EqualsTest::BAM);
35 const char* EqualsTest::READ_NAMES[] =
36 {
"01:====",
"02:===X",
"03:==X=",
"04:==XX",
"05:=X==",
"06:=X=X",
37 "07:=XX=",
"08:=XXX",
"09:X===",
"10:X==X",
"11:X=X=",
"12:X=XX",
38 "13:XX==",
"14:XX=X",
"15:XXX=",
"16:XXXX",
"Read:GGCCTA;Ref:CCTA",
39 "Read:CCTA;Ref:CCTA",
"Read:CCGTxxxC;Ref:CCxTAACC",
40 "Read:CCxxAC;Ref:CCTAACC",
"chromNotInRef",
"chromNotInRef1"};
42 const char* EqualsTest::READ_SEQS_BASES[] =
43 {
"CCTA",
"CCTT",
"CCAA",
"CCAT",
"CTTA",
"CTTT",
"CTAA",
"CTAT",
"TCTA",
"TCTT",
"TCAA",
"TCAT",
"TTTA",
"TTTT",
"TTAA",
"TTAT",
"GGCCTA",
44 "CCTA",
"CCGTC",
"CCAC",
"CCTA",
"CC=A"};
46 const char* EqualsTest::READ_SEQS_EQUALS[] =
47 {
"====",
"===T",
"==A=",
"==AT",
"=T==",
"=T=T",
"=TA=",
"=TAT",
"T===",
"T==T",
"T=A=",
"T=AT",
"TT==",
"TT=T",
"TTA=",
"TTAT",
"GG====",
48 "====",
"==G==",
"====",
"CCTA",
"CC=A"};
50 const char* EqualsTest::READ_SEQS_MIXED[] =
51 {
"C===",
"=C=T",
"==AA",
"==AT",
"=TTA",
"CT=T",
"=TAA",
"=TAT",
"T=TA",
"TC=T",
"TCA=",
"TCAT",
"TT=A",
"TT=T",
"TTA=",
"TTAT",
"GGC=T=",
52 "C=T=",
"C=GT=",
"C=A=",
"CCTA",
"CC=A"};
54 const char* EqualsTest::expectedReferenceName;
55 const char* EqualsTest::expectedMateReferenceName;
56 const char* EqualsTest::expectedMateReferenceNameOrEqual;
57 const char* EqualsTest::expectedCigar;
58 const char* EqualsTest::expectedQuality;
60 std::vector<unsigned int> EqualsTest::expectedCigarHex;
62 int EqualsTest::expected0BasedAlignmentEnd;
63 int EqualsTest::expected1BasedAlignmentEnd;
64 int EqualsTest::expectedAlignmentLength;
65 int EqualsTest::expected0BasedUnclippedStart;
66 int EqualsTest::expected1BasedUnclippedStart;
67 int EqualsTest::expected0BasedUnclippedEnd;
68 int EqualsTest::expected1BasedUnclippedEnd;
71 void EqualsTest::testEq(
FileType inputType)
76 std::string outputBase =
"results/out";
81 outputBase +=
"SamEq";
86 outputBase +=
"BamEq";
93 std::string outputName = outputBase +
"Bases.sam";
95 outputName = outputBase +
"Equals.sam";
97 outputName = outputBase +
"Orig.sam";
99 outputName = outputBase +
"Bases.bam";
101 outputName = outputBase +
"Equals.bam";
103 outputName = outputBase +
"Orig.bam";
105 assert(outBasesSam.WriteHeader(samHeader));
106 assert(outEqualsSam.WriteHeader(samHeader));
107 assert(outOrigSam.WriteHeader(samHeader));
108 assert(outBasesBam.WriteHeader(samHeader));
109 assert(outEqualsBam.WriteHeader(samHeader));
110 assert(outOrigBam.WriteHeader(samHeader));
131 for(
int j = 0; j < 16; j++)
133 assert(inSam.
ReadRecord(samHeader, samRecord) ==
true);
134 validateEqRead(samRecord, j, READ_SEQS_BASES[j]);
135 assert(outBasesSam.WriteRecord(samHeader, samRecord));
136 assert(outEqualsSam.WriteRecord(samHeader, samRecord));
137 assert(outOrigSam.WriteRecord(samHeader, samRecord));
138 assert(outBasesBam.WriteRecord(samHeader, samRecord));
139 assert(outEqualsBam.WriteRecord(samHeader, samRecord));
140 assert(outOrigBam.WriteRecord(samHeader, samRecord));
142 for(
int j = 0; j < 16; j++)
144 assert(inSam.
ReadRecord(samHeader, samRecord) ==
true);
145 validateEqRead(samRecord, j, READ_SEQS_EQUALS[j]);
146 assert(outBasesSam.WriteRecord(samHeader, samRecord));
147 assert(outEqualsSam.WriteRecord(samHeader, samRecord));
148 assert(outOrigSam.WriteRecord(samHeader, samRecord));
149 assert(outBasesBam.WriteRecord(samHeader, samRecord));
150 assert(outEqualsBam.WriteRecord(samHeader, samRecord));
151 assert(outOrigBam.WriteRecord(samHeader, samRecord));
153 for(
int j = 0; j < 16; j++)
155 assert(inSam.
ReadRecord(samHeader, samRecord) ==
true);
156 validateEqRead(samRecord, j, READ_SEQS_MIXED[j]);
157 assert(outBasesSam.WriteRecord(samHeader, samRecord));
158 assert(outEqualsSam.WriteRecord(samHeader, samRecord));
159 assert(outOrigSam.WriteRecord(samHeader, samRecord));
160 assert(outBasesBam.WriteRecord(samHeader, samRecord));
161 assert(outEqualsBam.WriteRecord(samHeader, samRecord));
162 assert(outOrigBam.WriteRecord(samHeader, samRecord));
165 expectedCigar =
"2S4M";
166 expectedCigarHex.clear();
167 expectedCigarHex.push_back(0x24);
168 expectedCigarHex.push_back(0x40);
169 expected0BasedUnclippedStart = expectedRecord.myPosition-2;
170 expected1BasedUnclippedStart = expected0BasedUnclippedStart + 1;
171 expectedRecord.myBlockSize = 70;
172 expectedRecord.myReadNameLength = 21;
173 expectedRecord.myCigarLength = 2;
174 expectedRecord.myReadLength = 6;
175 expectedQuality =
"??I00?";
176 assert(inSam.
ReadRecord(samHeader, samRecord) ==
true);
177 validateEqRead(samRecord, 16, READ_SEQS_MIXED[16]);
178 assert(outBasesSam.WriteRecord(samHeader, samRecord));
179 assert(outEqualsSam.WriteRecord(samHeader, samRecord));
180 assert(outOrigSam.WriteRecord(samHeader, samRecord));
181 assert(outBasesBam.WriteRecord(samHeader, samRecord));
182 assert(outEqualsBam.WriteRecord(samHeader, samRecord));
183 assert(outOrigBam.WriteRecord(samHeader, samRecord));
185 expectedCigar =
"4M4H";
186 expectedCigarHex.clear();
187 expectedCigarHex.push_back(0x40);
188 expectedCigarHex.push_back(0x45);
189 expected0BasedUnclippedStart = expectedRecord.myPosition;
190 expected1BasedUnclippedStart = expected0BasedUnclippedStart + 1;
191 expected0BasedUnclippedEnd = expectedRecord.myPosition + 7;
192 expected1BasedUnclippedEnd = expected0BasedUnclippedEnd + 1;
193 expectedRecord.myBlockSize = 65;
194 expectedRecord.myReadNameLength = 19;
195 expectedRecord.myCigarLength = 2;
196 expectedRecord.myReadLength = 4;
197 expectedQuality =
"I00?";
198 assert(inSam.
ReadRecord(samHeader, samRecord) ==
true);
199 validateEqRead(samRecord, 17, READ_SEQS_MIXED[17]);
200 assert(outBasesSam.WriteRecord(samHeader, samRecord));
201 assert(outEqualsSam.WriteRecord(samHeader, samRecord));
202 assert(outOrigSam.WriteRecord(samHeader, samRecord));
203 assert(outBasesBam.WriteRecord(samHeader, samRecord));
204 assert(outEqualsBam.WriteRecord(samHeader, samRecord));
205 assert(outOrigBam.WriteRecord(samHeader, samRecord));
207 expectedCigar =
"1M1P1M1I1M3D1M";
208 expectedCigarHex.clear();
209 expectedCigarHex.push_back(0x10);
210 expectedCigarHex.push_back(0x16);
211 expectedCigarHex.push_back(0x10);
212 expectedCigarHex.push_back(0x11);
213 expectedCigarHex.push_back(0x10);
214 expectedCigarHex.push_back(0x32);
215 expectedCigarHex.push_back(0x10);
216 expected0BasedAlignmentEnd = expectedRecord.myPosition + 6;
217 expected1BasedAlignmentEnd = expected0BasedAlignmentEnd + 1;
218 expectedAlignmentLength = 7;
219 expected0BasedUnclippedStart = expectedRecord.myPosition;
220 expected1BasedUnclippedStart = expected0BasedUnclippedStart + 1;
221 expected0BasedUnclippedEnd = expected0BasedAlignmentEnd;
222 expected1BasedUnclippedEnd = expected0BasedUnclippedEnd + 1;
223 expectedRecord.myBlockSize = 95;
224 expectedRecord.myReadNameLength = 27;
225 expectedRecord.myCigarLength = 7;
226 expectedRecord.myReadLength = 5;
227 expectedQuality =
"I00??";
228 assert(inSam.
ReadRecord(samHeader, samRecord) ==
true);
229 validateEqRead(samRecord, 18, READ_SEQS_MIXED[18]);
230 assert(outBasesSam.WriteRecord(samHeader, samRecord));
231 assert(outEqualsSam.WriteRecord(samHeader, samRecord));
232 assert(outOrigSam.WriteRecord(samHeader, samRecord));
233 assert(outBasesBam.WriteRecord(samHeader, samRecord));
234 assert(outEqualsBam.WriteRecord(samHeader, samRecord));
235 assert(outOrigBam.WriteRecord(samHeader, samRecord));
237 expectedCigar =
"2M2N2M";
238 expectedCigarHex.clear();
239 expectedCigarHex.push_back(0x20);
240 expectedCigarHex.push_back(0x23);
241 expectedCigarHex.push_back(0x20);
242 expected0BasedAlignmentEnd = expectedRecord.myPosition + 5;
243 expected1BasedAlignmentEnd = expected0BasedAlignmentEnd + 1;
244 expectedAlignmentLength = 6;
245 expected0BasedUnclippedStart = expectedRecord.myPosition;
246 expected1BasedUnclippedStart = expected0BasedUnclippedStart + 1;
247 expected0BasedUnclippedEnd = expected0BasedAlignmentEnd;
248 expected1BasedUnclippedEnd = expected0BasedUnclippedEnd + 1;
249 expectedRecord.myBlockSize = 74;
250 expectedRecord.myReadNameLength = 24;
251 expectedRecord.myCigarLength = 3;
252 expectedRecord.myReadLength = 4;
253 expectedQuality =
"I00?";
254 assert(inSam.
ReadRecord(samHeader, samRecord) ==
true);
255 validateEqRead(samRecord, 19, READ_SEQS_MIXED[19]);
256 assert(outBasesSam.WriteRecord(samHeader, samRecord));
257 assert(outEqualsSam.WriteRecord(samHeader, samRecord));
258 assert(outOrigSam.WriteRecord(samHeader, samRecord));
259 assert(outBasesBam.WriteRecord(samHeader, samRecord));
260 assert(outEqualsBam.WriteRecord(samHeader, samRecord));
261 assert(outOrigBam.WriteRecord(samHeader, samRecord));
266 assert(queryIter.getNextMatchMismatch(matchTest) ==
true);
267 assert(matchTest.
getType() == SamSingleBaseMatchInfo::MATCH);
269 assert(queryIter.getNextMatchMismatch(matchTest) ==
true);
270 assert(matchTest.
getType() == SamSingleBaseMatchInfo::MATCH);
272 assert(queryIter.getNextMatchMismatch(matchTest) ==
true);
273 assert(matchTest.
getType() == SamSingleBaseMatchInfo::MATCH);
275 assert(queryIter.getNextMatchMismatch(matchTest) ==
true);
276 assert(matchTest.
getType() == SamSingleBaseMatchInfo::MATCH);
278 assert(queryIter.getNextMatchMismatch(matchTest) ==
false);
283 expectedRecord.myBlockSize = 56;
284 expectedRecord.myReadNameLength = 14;
285 expectedRecord.myReferenceID = 1;
286 expectedReferenceName =
"2";
287 expectedRecord.myMateReferenceID = 1;
288 expectedMateReferenceName =
"2";
290 assert(inSam.
ReadRecord(samHeader, samRecord) ==
true);
291 validateEqRead(samRecord, 20, READ_SEQS_MIXED[20]);
292 assert(outBasesSam.WriteRecord(samHeader, samRecord));
293 assert(outEqualsSam.WriteRecord(samHeader, samRecord));
294 assert(outOrigSam.WriteRecord(samHeader, samRecord));
295 assert(outBasesBam.WriteRecord(samHeader, samRecord));
296 assert(outEqualsBam.WriteRecord(samHeader, samRecord));
297 assert(outOrigBam.WriteRecord(samHeader, samRecord));
302 expectedRecord.myBlockSize = 57;
303 expectedRecord.myReadNameLength = 15;
304 expectedRecord.myReferenceID = 1;
305 expectedReferenceName =
"2";
306 expectedRecord.myMateReferenceID = 1;
307 expectedMateReferenceName =
"2";
309 assert(inSam.
ReadRecord(samHeader, samRecord) ==
true);
310 validateEqRead(samRecord, 21, READ_SEQS_MIXED[21]);
311 assert(outBasesSam.WriteRecord(samHeader, samRecord));
312 assert(outEqualsSam.WriteRecord(samHeader, samRecord));
313 assert(outOrigSam.WriteRecord(samHeader, samRecord));
314 assert(outBasesBam.WriteRecord(samHeader, samRecord));
315 assert(outEqualsBam.WriteRecord(samHeader, samRecord));
316 assert(outOrigBam.WriteRecord(samHeader, samRecord));
319 assert(queryIter2.getNextMatchMismatch(matchTest) ==
false);
323 void EqualsTest::reset()
325 expectedReferenceName =
"1";
326 expectedMateReferenceName =
"1";
327 expectedMateReferenceNameOrEqual =
"=";
328 expectedCigar =
"4M";
329 expectedQuality =
"I00?";
332 expectedCigarHex.clear();
333 expectedCigarHex.push_back(0x40);
335 expectedRecord.myBlockSize = 50;
336 expectedRecord.myReferenceID = 0;
337 expectedRecord.myPosition = 10010;
338 expectedRecord.myReadNameLength = 8;
339 expectedRecord.myMapQuality = 0;
340 expectedRecord.myBin = 4681;
341 expectedRecord.myCigarLength = 1;
342 expectedRecord.myFlag = 73;
343 expectedRecord.myReadLength = 4;
344 expectedRecord.myMateReferenceID = 0;
345 expectedRecord.myMatePosition = 10008;
346 expectedRecord.myInsertSize = 0;
348 expected0BasedAlignmentEnd = 10013;
349 expected1BasedAlignmentEnd = expected0BasedAlignmentEnd + 1;
350 expectedAlignmentLength = 4;
351 expected0BasedUnclippedStart = expectedRecord.myPosition;
352 expected1BasedUnclippedStart = expected0BasedUnclippedStart + 1;
353 expected0BasedUnclippedEnd = expected0BasedAlignmentEnd;
354 expected1BasedUnclippedEnd = expected1BasedAlignmentEnd;
357 void EqualsTest::validateEqRead(
SamRecord& samRecord,
359 const char* actualExpectedSequence)
377 assert(samRecord.
getBlockSize() == expectedRecord.myBlockSize);
378 assert(samRecord.
getReferenceID() == expectedRecord.myReferenceID);
383 expectedRecord.myReadNameLength);
384 assert(samRecord.
getMapQuality() == expectedRecord.myMapQuality);
385 assert(samRecord.
getBin() == expectedRecord.myBin);
386 assert(samRecord.
getCigarLength() == expectedRecord.myCigarLength);
387 assert(samRecord.
getFlag() == expectedRecord.myFlag);
388 assert(samRecord.
getReadLength() == expectedRecord.myReadLength);
390 expectedRecord.myMateReferenceID);
392 expectedMateReferenceName) == 0);
394 expectedMateReferenceNameOrEqual) == 0);
396 expectedRecord.myMatePosition + 1);
398 expectedRecord.myMatePosition);
399 assert(samRecord.
getInsertSize() == expectedRecord.myInsertSize);
400 assert(strcmp(samRecord.
getReadName(), READ_NAMES[readIndex]) == 0);
401 assert(strcmp(samRecord.
getCigar(), expectedCigar) == 0);
403 assert(strcmp(samRecord.
getSequence(), READ_SEQS_BASES[readIndex]) == 0);
404 assert(strcmp(samRecord.
getQuality(), expectedQuality) == 0);
406 assert(samRecord.
getSequence(0) == READ_SEQS_BASES[readIndex][0]);
407 assert(samRecord.
getQuality(0) == expectedQuality[0]);
408 assert(samRecord.
getSequence(1)== READ_SEQS_BASES[readIndex][1]);
409 assert(samRecord.
getQuality(1) == expectedQuality[1]);
410 assert(samRecord.
getSequence(2) == READ_SEQS_BASES[readIndex][2]);
411 assert(samRecord.
getQuality(2) == expectedQuality[2]);
412 assert(samRecord.
getSequence(3) == READ_SEQS_BASES[readIndex][3]);
413 assert(samRecord.
getQuality(3) == expectedQuality[3]);
416 READ_SEQS_EQUALS[readIndex]) == 0);
418 READ_SEQS_EQUALS[readIndex][0]);
419 assert(samRecord.
getQuality(0) == expectedQuality[0]);
421 READ_SEQS_EQUALS[readIndex][1]);
422 assert(samRecord.
getQuality(1) == expectedQuality[1]);
424 READ_SEQS_EQUALS[readIndex][2]);
425 assert(samRecord.
getQuality(2) == expectedQuality[2]);
427 READ_SEQS_EQUALS[readIndex][3]);
428 assert(samRecord.
getQuality(3) == expectedQuality[3]);
431 actualExpectedSequence) == 0);
433 actualExpectedSequence[0]);
434 assert(samRecord.
getQuality(0) == expectedQuality[0]);
436 actualExpectedSequence[1]);
437 assert(samRecord.
getQuality(1) == expectedQuality[1]);
439 actualExpectedSequence[2]);
440 assert(samRecord.
getQuality(2) == expectedQuality[2]);
442 actualExpectedSequence[3]);
443 assert(samRecord.
getQuality(3) == expectedQuality[3]);
447 actualExpectedSequence) == 0);
449 actualExpectedSequence[0]);
450 assert(samRecord.
getQuality(0) == expectedQuality[0]);
452 actualExpectedSequence[1]);
453 assert(samRecord.
getQuality(1) == expectedQuality[1]);
455 actualExpectedSequence[2]);
456 assert(samRecord.
getQuality(2) == expectedQuality[2]);
458 actualExpectedSequence[3]);
459 assert(samRecord.
getQuality(3) == expectedQuality[3]);
467 validateEqReadBuffer(samRecord, READ_SEQS_BASES[readIndex]);
469 validateEqReadBuffer(samRecord, actualExpectedSequence);
471 validateEqReadBuffer(samRecord, READ_SEQS_EQUALS[readIndex]);
475 void EqualsTest::validateEqReadBuffer(
SamRecord& samRecord,
476 const char* expectedSequence)
479 unsigned char* varPtr;
483 assert(bufferPtr->myBlockSize == expectedRecord.myBlockSize);
484 assert(bufferPtr->myReferenceID == expectedRecord.myReferenceID);
485 assert(bufferPtr->myPosition == expectedRecord.myPosition);
486 assert(bufferPtr->myReadNameLength == expectedRecord.myReadNameLength);
487 assert(bufferPtr->myMapQuality == expectedRecord.myMapQuality);
488 assert(bufferPtr->myBin == expectedRecord.myBin);
489 assert(bufferPtr->myCigarLength == expectedRecord.myCigarLength);
490 assert(bufferPtr->myFlag == expectedRecord.myFlag);
491 assert(bufferPtr->myReadLength == expectedRecord.myReadLength);
492 assert(bufferPtr->myMateReferenceID ==
493 expectedRecord.myMateReferenceID);
494 assert(bufferPtr->myMatePosition == expectedRecord.myMatePosition);
495 assert(bufferPtr->myInsertSize == expectedRecord.myInsertSize);
499 varPtr = (
unsigned char*)(&(bufferPtr->myData[0]));
502 for(
int i = 0; i < expectedRecord.myReadNameLength; i++)
509 for(
int i = 0; i < expectedRecord.myCigarLength; i++)
511 assert(*(
unsigned int*)varPtr == expectedCigarHex[i]);
517 int expectedSeqHex = 0;
518 for(
int i = 0; i < expectedRecord.myReadLength; i++)
521 switch(expectedSequence[i])
549 expectedSeqHex = hexChar << 4;
553 expectedSeqHex |= hexChar;
554 assert(*varPtr == expectedSeqHex);
558 if((expectedRecord.myReadLength%2) != 0)
561 assert(*varPtr == expectedSeqHex);
566 for(
int i = 0; i < expectedRecord.myReadLength; i++)
568 assert(*varPtr == samRecord.
getQuality()[i] - 33);
Create/Access/Modify/Load Genome Sequences stored as binary mapped files.
Allows the user to easily read/write a SAM/BAM file.
bool ReadHeader(SamFileHeader &header)
Reads the header section from the file and stores it in the passed in header.
bool ReadRecord(SamFileHeader &header, SamRecord &record)
Reads the next record from the file & stores it in the passed in record.
void SetReference(GenomeSequence *reference)
Sets the reference to the specified genome sequence object.
bool OpenForRead(const char *filename, SamFileHeader *header=NULL)
Open a sam/bam file for reading with the specified filename, determing the type of file and SAM/BAM b...
Iterates through the query and compare with reference.
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record.
int32_t getBlockSize()
Get the block size of the record (BAM format).
uint16_t getCigarLength()
Get the length of the BAM formatted CIGAR.
const char * getReferenceName()
Get the reference sequence name (RNAME) of the record.
@ NONE
Leave the sequence as is.
@ BASES
Translate '=' to the actual base.
@ EQUAL
Translate bases that match the reference to '='.
int32_t getInsertSize()
Get the inferred insert size of the read pair (ISIZE) or observed template length (TLEN).
int32_t get0BasedMatePosition()
Get the 0-based(BAM) leftmost mate/next fragment's position.
int32_t get1BasedPosition()
Get the 1-based(SAM) leftmost position (POS) of the record.
int32_t getReferenceID()
Get the reference sequence id of the record (BAM format rid).
int32_t getAlignmentLength()
Returns the length of the clipped sequence, returning 0 if the cigar is '*'.
int32_t get1BasedAlignmentEnd()
Returns the 1-based inclusive rightmost position of the clipped sequence.
uint8_t getReadNameLength()
Get the length of the readname (QNAME) including the null.
const char * getMateReferenceNameOrEqual()
Get the mate/next fragment's reference sequence name (RNEXT), returning "=" if it is the same as the ...
int32_t get1BasedUnclippedStart()
Returns the 1-based inclusive left-most position adjusted for clipped bases.
uint16_t getBin()
Get the BAM bin for the record.
int32_t getMateReferenceID()
Get the mate reference id of the record (BAM format: mate_rid/next_refID).
uint16_t getFlag()
Get the flag (FLAG).
const void * getRecordBuffer()
Get a const pointer to the buffer that contains the BAM representation of the record.
void setSequenceTranslation(SequenceTranslation translation)
Set the type of sequence translation to use when getting the sequence.
int32_t get1BasedMatePosition()
Get the 1-based(SAM) leftmost mate/next fragment's position (PNEXT).
int32_t get0BasedUnclippedEnd()
Returns the 0-based inclusive right-most position adjusted for clipped bases.
int32_t get1BasedUnclippedEnd()
Returns the 1-based inclusive right-most position adjusted for clipped bases.
const char * getMateReferenceName()
Get the mate/next fragment's reference sequence name (RNEXT).
bool getNextSamTag(char *tag, char &vtype, void **value)
Get the next tag from the record.
int32_t get0BasedUnclippedStart()
Returns the 0-based inclusive left-most position adjusted for clipped bases.
int32_t getReadLength()
Get the length of the read.
int32_t get0BasedAlignmentEnd()
Returns the 0-based inclusive rightmost position of the clipped sequence.
int32_t get0BasedPosition()
Get the 0-based(BAM) leftmost position of the record.
const char * getCigar()
Returns the SAM formatted CIGAR string.
uint8_t getMapQuality()
Get the mapping quality (MAPQ) of the record.
const char * getReadName()
Returns the SAM formatted Read Name (QNAME).
const char * getQuality()
Returns the SAM formatted quality string (QUAL).
const char * getSequence()
Returns the SAM formatted sequence string (SEQ), translating the base as specified by setSequenceTran...
This class contains the match/mismatch information between the reference and a read for a single base...
int32_t getQueryIndex()
Get the query index for this object.
Type getType()
Get the type (match/mismatch/unknown) for this object.
Structure of a BAM record.