createBamPath: create a bam path

In cmatKhan/brentlabRnaSeqTools: A Collection of Functions to Interact with the Brentlab RNASeq Database

Description

a helper function to create a bampath from some metadata information. Also checks if index exists

Usage

createBamPath(
  run_number,
  fastq_filename,
  align_expr_prefix,
  bam_suffix = "_sorted_aligned_reads_with_annote.bam",
  test = FALSE
)

Arguments

run_number	the run_number (mind the leading zeros for old runs) of the run
fastq_filename	the fastq filename, preferrably without the extension or any leading path info. However, an effort has been made to deal with full paths and extensions
align_expr_prefix	the location of the run directories. Eg, if you are mounted and on your local computer, it might be something like "/mnt/htcf_lts/lts_align_expr"
bam_suffix	the common bam suffix for all bam files stored in /lts. Default is "_sorted_aligned_reads_with_annote.bam"
test	boolean, default FALSE. Set to TRUE if testing this function

Value

a verified filepath to the bam file

cmatKhan/brentlabRnaSeqTools documentation built on Nov. 17, 2021, 5:47 a.m.