chimera (version 1.14.0)

validateSamFile: A function to validate SAM or BAM files

Description

A function to validate SAM or BAM files using picard-tools

Usage

validateSamFile(input, output, mode=c("VERBOSE", "SUMMARY"), max.output="100")

Arguments

input

SAM/BAM file to be validated

output

file name in which to save the validation information

mode

Mode of output. Default value: VERBOSE

max.output

max number of reported error lines

Value

Validation information referring to a SAM/BM file.

See Also

picardInstallation

Examples

#validateSamFile(input=paste(find.package(package="chimera"),"/examples/mcf7_trs_accepted_hits.bam",sep=""), output="validation_results.txt", mode="SUMMARY", max.output="100")