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< TestPileupElement > | myAnalyzeFuncPtr |
| std::vector< TestPileupElement > | myElements |
| int | pileupStart |
| int | pileupHead |
| int | pileupTail |
| int | pileupWindow |
| int | myCurrentRefID |
| GenomeSequence * | myRefPtr |
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:
- bam/test/TestPileup.h
- bam/test/TestPileup.cpp
