get_consensus_df: Get the consenus sequence of the read hits to the reference
In jkruppa/virDisco: Modules for a viral detection pipeline

Description Usage Arguments Details Value Author(s)

Caution! This function will take much time, because it is only optimised for small sequences.

1	get_consensus_df(hits, out_file, par_list)

`hits`	Genebank IDs of the hits
`out_file`	File path to the results dir
`par_list`	Parameter given by the par_list(), see `set_par_list`

This function is based on samtools to get the reference to the hit. Further the consensus is generated by adding blanks "-" to the start and the end of the reads to cover the full reference. Therefore, it will be very slow, if the reference becomes very large.

data.frame

Jochen Kruppa

jkruppa/virDisco documentation built on May 3, 2019, 7:05 p.m.