RandomAccessManager

Class which random access tasks are delegated to.

class RandomAccessManager {

void setTaskPool(TaskPool task_pool);

void setBufferSize(size_t buffer_size);

this(string filename);

this(BamReader reader);

this(string filename, BaiFile bai);

this(BamReader reader, BaiFile bai);

VirtualOffset eofVirtualOffset();

bool hasEofBlock();

BgzfInputStream createStreamStartingFrom(VirtualOffset offset);

BamRead getReadAt(VirtualOffset offset);

BgzfBlock getBgzfBlockAt(ulong offset);

auto getReadsBetween(VirtualOffset from, VirtualOffset to);

bool found_index_file();

const(BaiFile) getBai();

Chunk[] getChunks(BamRegion region);

auto getReads(BamRegion region);

auto getReads(BamRegion[] regions);

struct BamReadFilter(R);

static auto filterBamReads(R r, BamRegion[] regions);

}

Constructors

this this(string filename)
this(BamReader reader): Constructs new manager for BAM file
this this(string filename, BaiFile bai)
this(BamReader reader, BaiFile bai): Constructs new manager with given index file. This allows to do random-access interval queries.

Members

Functions

createStreamStartingFrom BgzfInputStream createStreamStartingFrom(VirtualOffset offset): Get new BgzfInputStream starting from specified virtual offset.
eofVirtualOffset VirtualOffset eofVirtualOffset(): If file ends with EOF block, returns virtual offset of the start of EOF block. Otherwise, returns virtual offset of the physical end of file.
found_index_file bool found_index_file(): Undocumented in source. Be warned that the author may not have intended to support it.
getBai const(BaiFile) getBai(): BAI file
getBgzfBlockAt BgzfBlock getBgzfBlockAt(ulong offset): Get BGZF block at a given offset.
getChunks Chunk[] getChunks(BamRegion region): Get BAI chunks containing all alignment records overlapping the region
getReadAt BamRead getReadAt(VirtualOffset offset): Get single read at a given virtual offset. Every time new stream is used.
getReads auto getReads(BamRegion region): Fetch alignments with given reference sequence id, overlapping [beg..end)
getReads auto getReads(BamRegion[] regions): Undocumented in source. Be warned that the author may not have intended to support it.
getReadsBetween auto getReadsBetween(VirtualOffset from, VirtualOffset to): Get reads between two virtual offsets. First virtual offset must point to a start of an alignment record.
hasEofBlock bool hasEofBlock(): Returns true if the file ends with EOF block, and false otherwise.
setBufferSize void setBufferSize(size_t buffer_size): Undocumented in source. Be warned that the author may not have intended to support it.
setTaskPool void setTaskPool(TaskPool task_pool): Undocumented in source. Be warned that the author may not have intended to support it.

Static functions

filterBamReads auto filterBamReads(R r, BamRegion[] regions): Undocumented in source. Be warned that the author may not have intended to support it.

Structs

BamReadFilter struct BamReadFilter(R): Undocumented in source.

Meta

Source

See Implementation

bio std hts bam randomaccessmanager classes

RandomAccessManager