18 #ifndef __BAM_INDEX_H__ 19 #define __BAM_INDEX_H__ 26 #include "IndexBase.h" 29 #include "SamStatus.h" 53 uint64_t getMaxOffset()
const;
62 uint64_t& maxOffset)
const;
79 void printIndex(int32_t refID,
bool summary =
false);
92 uint64_t maxOverallOffset;
94 int32_t myUnMappedNumReads;
void printIndex(int32_t refID, bool summary=false)
Print the index information.
static const int32_t REF_ID_ALL
The number used to indicate that all reference ids should be used.
int32_t getNumUnMappedReads(int32_t refID)
Get the number of unmapped reads for this reference id.
bool getReferenceMinMax(int32_t refID, uint64_t &minOffset, uint64_t &maxOffset) const
Get the minimum and maximum file offsets for the specfied reference ID.
SamStatus::Status readIndex(const char *filename)
int32_t getNumMappedReads(int32_t refID)
Get the number of mapped reads for this reference id.
virtual void resetIndex()
Reset the member data for a new index file.
bool getChunksForRegion(int32_t refID, int32_t start, int32_t end, SortedChunkList &chunkList)
Get the list of chunks associated with this region.
static const int32_t UNKNOWN_NUM_READS
The number used for an unknown number of reads.
Status
Return value enum for StatGenFile methods.
static const int32_t REF_ID_UNMAPPED
The number used for the reference id of unmapped reads.