[BioC] ShortRead qa() for BAM files?

Hollis Wright wrighth at ohsu.edu
Wed Oct 6 21:55:09 CEST 2010

Hello, all; is there no qa() function in ShortRead for BAM files? I've noticed there is no BAM-specific qa function in the documentation for ShortRead. I've imported a BAM representing a single lane on a Illumina IIGA run after alignment with Bowtie and conversion of SAM to BAM with samtools thus: 

params <- ScanBamParam(scanBamFlag(isUnmappedQuery=FALSE), what=scanBamWhat())
lane1 <- readAligned("s_1_sequence.txt.sorted.bam.bam", type="BAM", param=params)

which reads in ok, but qa complains:

Error: UserArgumentMismatch
  'lane' must be 'character(1)'

Is this because there is no function to handle BAM files? Or is this some problem with the file itself or with only using a single read? For what it's worth, coverage runs fine on this object.

Hollis Wright, PhD
Oregon Clinical and Translational Research Institute

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