validateSamFile {chimera} | R Documentation

## 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.

### Author(s)

Raffaele A Calogero

### 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")

[Package chimera version 1.26.0 Index]