count_substring_fixed: Count sequence content in a given sequence.

In kmeRtone: Multi-Purpose and Flexible k-Meric Enrichment Analysis Software

Count sequence content in a given sequence.

Description

stringi has no function that search within substring without memory copy it. This function has two versions. One without the need to memory copy denoted as ***. The only downside to this is std::string::find cannot stop searching past end of substring. I manage to at least stop it as soon as possible. If the pattern is long and rare, it won't stop until it find post-substring pattern. The other version is memory copy substring but as this operation is in the loop, the memory is still within comfortable range. c++17 has std::string_view that solve this but still new and not widely available. Use count_substring_regex to avoid memory copy.

Usage

count_substring_fixed(sequence, start, end, pattern)

Arguments

sequence	A sequence to map.
start	Start positions.
end	End positions.
pattern	A pattern to search for.

Value

A numeric vector of count.

kmeRtone documentation built on Sept. 11, 2024, 9:12 p.m.