libStatGen Software 1
TestPileup Class Reference
Inheritance diagram for TestPileup:
Collaboration diagram for TestPileup:

Public Member Functions

void testPileupPosition ()
 
- Public Member Functions inherited from Pileup< TestPileupElement >
 Pileup (const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >())
 Constructor using the default maximum number of bases a read spans. More...
 
 Pileup (int window, const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >())
 Constructor that sets the maximum number of bases a read spans. More...
 
 Pileup (const std::string &refSeqFileName, const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >())
 Perform pileup with a reference. More...
 
 Pileup (int window, const std::string &refSeqFileName, const defaultPileup< TestPileupElement > &fp=defaultPileup< TestPileupElement >())
 Perform pileup with a reference and a specified window size. More...
 
virtual ~Pileup ()
 Destructor. More...
 
virtual int processFile (const std::string &fileName, uint16_t excludeFlag=0x0704, uint16_t includeFlag=0)
 Performs a pileup on the specified file. More...
 
virtual void processAlignment (SamRecord &record)
 Add an alignment to the pileup. More...
 
virtual void processAlignmentRegion (SamRecord &record, int startPos, int endPos, PosList *excludeList=NULL)
 Add only positions that fall within the specified region of the alignment to the pileup and outside of the specified excluded positions. More...
 
void flushPileup ()
 Done processing, flush every position that is currently being stored in the pileup. More...
 

Additional Inherited Members

- Protected Member Functions inherited from Pileup< TestPileupElement >
virtual void flushPileup (int refID, int refPosition)
 
void flushPileup (int refPosition)
 
void addAlignmentPosition (int refPosition, SamRecord &record)
 
int pileupPosition (int refPosition)
 
virtual void resetElement (TestPileupElement &element, int position)
 
virtual void addElement (TestPileupElement &element, SamRecord &record)
 
virtual void analyzeElement (TestPileupElement &element)
 
virtual void analyzeHead ()
 
- Protected Attributes inherited from Pileup< TestPileupElement >
defaultPileup< TestPileupElementmyAnalyzeFuncPtr
 
std::vector< TestPileupElementmyElements
 
int pileupStart
 
int pileupHead
 
int pileupTail
 
int pileupWindow
 
int myCurrentRefID
 
GenomeSequencemyRefPtr
 

Detailed Description

Definition at line 32 of file TestPileup.h.

Member Function Documentation

◆ testPileupPosition()

void TestPileup::testPileupPosition ( )

Definition at line 32 of file TestPileup.cpp.

33{
34 assert(pileupPosition(14000) == 0);
35 assert(pileupHead == 14000);
36 assert(pileupStart == 14000);
37 assert(pileupTail == 14000);
38
39 bool caught = false;
40 try
41 {
42 pileupPosition(13999);
43 }
44 catch(std::exception& e)
45 {
46 caught = true;
47 assert(strcmp(e.what(), "Overflow on the pileup buffer: specifiedPosition = 13999, pileup buffer start position: 14000, pileup buffer end position: 15024") == 0);
48 }
49 assert(caught);
50
51 caught = false;
52 try
53 {
54 pileupPosition(15025);
55 }
56 catch(std::exception& e)
57 {
58 caught = true;
59 assert(strcmp(e.what(), "Overflow on the pileup buffer: specifiedPosition = 15025, pileup buffer start position: 14000, pileup buffer end position: 15024") == 0);
60 }
61 assert(caught);
62}

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