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))
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...
bool WriteHeader(SamFileHeader &header)
Writes the specified header into the file.
bool ReadHeader(SamFileHeader &header)
Reads the header section from the file and stores it in the passed in header.
bool shiftIndelsLeft()
Shift the indels (if any) to the left by updating the CIGAR.
Allows the user to easily read/write a SAM/BAM file.