18 #include "ShiftIndels.h" 21 void testShiftIndels()
23 ShiftIndelsTest::testShift(
"testFiles/testShift.sam",
"results/testShift.sam");
24 #ifdef __ZLIB_AVAILABLE__ 25 ShiftIndelsTest::testShift(
"testFiles/testShift.bam",
"results/testShift.bam");
26 ShiftIndelsTest::testShift(
"testFiles/testShift.bam",
"results/testShiftFromBam.sam");
28 ShiftIndelsTest::testShift(
"testFiles/testShift.sam",
"results/testShiftFromSam.bam");
31 void ShiftIndelsTest::testShift(
const char* input,
const char* output)
47 bool shiftResult =
true;
50 if((readNum == 3)|| (readNum == 5))
60 assert(samRecord.shiftIndelsLeft() == shiftResult);
bool ReadHeader(SamFileHeader &header)
Reads the header section from the file and stores it in the passed in header.
Allows the user to easily read/write a SAM/BAM file.
bool WriteHeader(SamFileHeader &header)
Writes the specified header into the file.
bool WriteRecord(SamFileHeader &header, SamRecord &record)
Writes the specified record into the file.
bool ReadRecord(SamFileHeader &header, SamRecord &record)
Reads the next record from the file & stores it in the passed in record.
bool OpenForWrite(const char *filename, SamFileHeader *header=NULL)
Open a sam/bam file for writing with the specified filename, determining SAM/BAM from the extension (...
Class providing an easy to use interface to get/set/operate on the fields in a SAM/BAM record...
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...