Module bam::index[−][src]

BAI index, virtual offset and bgzip chunks.

Structs

Bin	Single bin that stores chunks within the BAM file.
BinsIter	Iterator over bins.
Chunk	Chunk `[start-end)`, where `start` and `end` are virtual offsets.
Index	BAI Index. Allows to get chunks in a bgzip file, that contain records from a specific genomic region.
LinearIndex	Stores linear index: for each tiling 16384bp window it stores the smallest file offset of an alignment that overlaps it.
Reference	Index for a single reference sequence. Contains bins and a linear index.
VirtualOffset	Virtual offset. Represents `block_offset << 16 \| contents_offset`, where `block_offset` is `u48` and represents the offset in the bgzip file to the beginning of the block (also known as `coffset` or `compressed_offset`).

Maximal possible bin value.

bin_to_region	Returns a maximal region for a given bin.
region_to_bin	Returns a BAI bin for the record with alignment `[beg-end)`.
region_to_bins	Returns all possible BAI bins for the region `[beg-end)`.