pileupChunks

This function constructs range of non-overlapping consecutive pileups from a range of reads so that these pileups can be processed in parallel.

It's allowed to pass ranges of sorted reads with different ref. IDs, they won't get mixed in any chunk.

pileupChunks
(
R
)
(,
bool use_md_tag = false
,
size_t block_size = 16_384_000
,
ulong start_from = 0
,
ulong end_at = ulong.max
)

Parameters

use_md_tag bool

recover reference bases from MD tag and CIGAR

block_size size_t

approximate amount of memory that each pileup will consume, given in bytes. (Usually consumption will be a bit higher.)

start_from ulong

position of the first column of the first chunk

end_at ulong

position after the last column of the last chunk


WARNING: block size should be big enough so that every block will share some reads only with adjacent blocks.
As such, it is not recommended to reduce the block_size. But there might be a need to increase it in case of very high coverage.

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