query_bam_index: Fetch sequence rows matching a given index value

In mskilab/bambi: R to query barcode indices on bam files

Description

Wrapper around bamdb functions to query an indexed bam file. This requires a prebuilt index for the specific bam file that contains the desired column.

Usage

  query_bam_index(bam_file_name, bam_index_path, index_name, key)

Arguments

bam_file_name	The path of the indexed sequence file
bam_index_path	The top level directory of the bamdb generated index
index_name	The name of indexed field to search in
key	The desired value of the indexed field

Value

Returns a data frame with all of the matching sequnce rows on success. The data frame will be empty of no results were found. If there is an error with querying the index or file the result will be null.

mskilab/bambi documentation built on May 14, 2019, 4:04 a.m.