query_table_rsamtools: Query tabular: 'Rsamtools'

In RajLabMSSM/echotabix: echoverse module: automated creation and querying of tabix files

Query tabular: Rsamtools

Description

Rsamtools can query both local and remote files. However, it seems unable to read the header of tabix files created with seqminer.

Usage

query_table_rsamtools(
  target_path,
  target_index = paste0(target_path, ".tbi"),
  query_granges,
  yieldSize = NA_character_,
  verbose = TRUE
)

Arguments

target_path	Path to tabix file.
target_index	Tabix index file for target_path.
query_granges	GRanges object to be used for querying the target_path file. Alternatively, can be variant-level summary statistics to be converted into a GRanges object by construct_query.
verbose	Print messages.

Source

Bugs in Rsamtools::scanTabix

RajLabMSSM/echotabix documentation built on Nov. 21, 2023, 8:02 a.m.