systemPicard: Calls the Picard executable

In HenrikBengtsson/aroma.seq: High-Throughput Sequence Analysis using the Aroma Framework

Description

Calls the Picard executable.

Usage

## Default S3 method:
systemPicard(command, ..., verbose=FALSE)

Arguments

command	A character string specifying the Picard command (the name of the jar file without the *.jar extension).
...	Additional arguments specifying Picard command line switches.
verbose	See Verbose.

Author(s)

Henrik Bengtsson

Examples

## Not run: 
  pathnameBAM <- "bwaData/LambdaVirusExample,bwa,is/Lambda_phage/reads_1.bam"
  res <- systemPicard("ValidateSamFile", INPUT=pathnameBAM, stderr=FALSE)
  ## ERROR: Read groups is empty
  print(res)
  ## [1] 1

  res <- systemPicard("ValidateSamFile", INPUT=pathnameBAM,
                      IGNORE="MISSING_READ_GROUP", stderr=FALSE)
  ## "No errors found"
  print(res)
  ## [1] 0

## End(Not run)

HenrikBengtsson/aroma.seq documentation built on Feb. 15, 2021, 2:21 a.m.