Dear all, I got a unexpected behaviour when I set the isValidVendorRead flag as TRUE. >library(Rsamtools) >ScanBamParam(flag=scanBamFlag(isValidVendorRead=TRUE)) class: ScanBamParam bamFlag (NA unless specified): isValidVendorRead=FALSE bamSimpleCigar: FALSE bamReverseComplement: FALSE bamTag: bamWhich: 0 elements bamWhat: The isValidVendorRead is shown as being FALSE but I would expect it to be TRUE. I started using Rsamtools recently so I am not sure if I am missing something or if this a bug. Thanks in advance for your time, Nuno Fonseca sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] Rsamtools_1.8.4 Biostrings_2.24.1 GenomicRanges_1.8.5 [4] IRanges_1.14.2 BiocGenerics_0.2.0 loaded via a namespace (and not attached): [1] bitops_1.0-4.1 stats4_2.15.0 zlibbioc_1.2.0

On 05/21/2012 03:19 AM, Nuno Fonseca wrote: > Dear all, > > I got a unexpected behaviour when I set the isValidVendorRead flag as TRUE. > > >library(Rsamtools) > >ScanBamParam(flag=scanBamFlag(isValidVendorRead=TRUE)) > class: ScanBamParam > bamFlag (NA unless specified): isValidVendorRead=FALSE > bamSimpleCigar: FALSE > bamReverseComplement: FALSE > bamTag: > bamWhich: 0 elements > bamWhat: > > The isValidVendorRead is shown as being FALSE but I would expect it to > be TRUE. I started using Rsamtools recently so I am not sure if I am > missing something or if this a bug. Hi Nuno -- this is a bug; setting scanBamFlag(isValidVendorRead=TRUE) has the effect documented on ?ScanBamParam -- only valid vendor reads are returned. The SAM / BAM specification (now) says the underlying flag is TRUE when reads do NOT pass quality checks, and in the development version of Bioconductor Rsamtools v.1.9.12 the flag 'isValidVendorRead' is deprecated in favor of 'isNotPassingQUalityControls', with TRUE and FALSE interchanged when the flag is created. The double negative (NOT ... FALSE) is consistent with the SAM / BAM specification. > ScanBamParam(flag=scanBamFlag(isNotPassingQualityControls=FALSE)) class: ScanBamParam bamFlag (NA unless specified): isNotPassingQualityControls=FALSE bamSimpleCigar: FALSE bamReverseComplement: FALSE bamTag: bamWhich: 0 elements bamWhat: Martin > > Thanks in advance for your time, > > Nuno Fonseca > > sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] Rsamtools_1.8.4 Biostrings_2.24.1 GenomicRanges_1.8.5 > [4] IRanges_1.14.2 BiocGenerics_0.2.0 > > loaded via a namespace (and not attached): > [1] bitops_1.0-4.1 stats4_2.15.0 zlibbioc_1.2.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793