Thanks Martin, I didn't quite understand that sentence: now it clear. My hope was indeed to be able to iterate by yieldSize within a prespecified range, without writing a new file to the disk (like filterBAM does...right?) Thanks Stefano On 06/17/2014 06:31 PM, Martin Morgan wrote: > On 06/17/2014 05:39 AM, Stefano Calza wrote: >> Hi! >> >> I am experiencing this weird (to me...) behaviour: >> >> bfl = BamFile(some/bam/file,yieldSize=100000L) >> >> param=ScanBamParam(which=RangesList(chr22=IRanges(1,51304566))) >> >> ## 1 >> readGAlignmentsFromBam(bfl) >> >> ## 2 >> >> readGAlignmentsFromBam(bfl,param=param) >> >> >> Now 1) is much faster than 2). Indeed 1) takes ~ 6 secs while 2) at >> least a >> couple of minutes till I killed it... >> >> Am I doing something wrong or missing something here? > > Hi Stefano -- > > Does the description on ?BamFile help? > > yieldSize: Number of records to yield each time the file is read > from using 'scanBam' or, when 'length(bamWhich()) != 0', a > threshold which yields records in complete ranges whose sum > first exceeds 'yieldSize'. > > you're getting the complete range chr22=IRanges(1,51304566), because > that will be the first complete range for which yieldSize is satsified. > > The current implementation allows you to iterate through an entire > file, or iterate through many small ranges, but it does not really > work well if the goal is to subset the bam file (e.g., by chromsome) > and iterate through the subset; you would then filterBam and iterate > through that. > > It could also be that there is a bug in the code; it would then help > to have the output of sessionInfo() and a reproducible example, e.g., > a subset of some/bam/file or use of the files in the experiment data > package RNAseqData.HNRNPC.bam.chr14 > > Martin > > >> >> Stefano >> >> _______________________________________________ >> 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 > >