Hi. I'm trying to do random sampling with R.
When I run 
   

    library(GenomicAlignments)
    library(rtracklayer)

    ## your bam file
    bam.file <- 'your_bam_file.bam'
    
    ## is it paired end or not
    paired <- TRUE
    
    ## read in the bam file
    if(paired){
      bam.input <- readGAlignmentPairs(bam.file)
    }else{
      bam.input <- readGAlignments(bam.file)
    }
    
    ## select your number of subsets
    num.samples <- 100
    
    ## subsample WITH replacement
    bam.subsample <- sample(bam.input,num.samples,replace=TRUE)
    
    ## export new bam file
    export(bam.subsample,BamFile('bam_subsampled.bam'))

I get the following error message 

    [E::hts_idx_push] Region 554468587..554468738 cannot be stored in a bai index. Try using a csi index with min_shift = 14, n_lvls >= 6
     value[[3L]](cond) でエラー: 'asBam' failed to build index
      file: bam_subsampled.bam
      SAM file: 'bam_subsampled.sam'
     追加情報:  警告メッセージ: 
     .make_GAlignmentPairs_from_GAlignments(gal, strandMode = strandMode,  で: 
        79328 alignments with ambiguous pairing were dumped.
        Use 'getDumpedAlignments()' to retrieve them from the dump environment.

I searched for csi option in Rsamtools or GenomicAlignmets, but I wasn't able to find that.

How can I solve this error ?? 
Thanks.
Simply add `index = FALSE` to avoid building the index. 

`export(bam.subsample,BamFile('bam_subsampled.bam'), index = FALSE)`

If you need the index you can create it with samtools at any time (`samtools index -c bam_subsampled.bam`)

Also asked for some details over at the BioC forum, see what they say. https://support.bioconductor.org/p/126603/