Hi,

I have found this recurrent error with RSamtools when loading alignments of load read data sets(PacBio/Oxford Nanopore):

what=c("qname","cigar")
param=ScanBamParam(what=what, tag=c("NM", "MD"))
bamf=BamFile(filey)
bam=scanBam(bamf, param=param)[[1]]

Error in value[[3L]](cond) :
   'Realloc' could not re-allocate memory (0 bytes)
   file: /mithril/Data/Nanopore/oxford/082814_lambdaunmeth/analysis/bwa400b.bam
   index:

I've included a bam file (https://www.dropbox.com/s/od6oeeuvzv8dlfj/bwa400b.bam?dl=0) which will cause this with a minimal number of reads (5) - the file itself is only ~80Kb - so I expect this is a character overrun in loading the cigar.  It seems that if I don't load the cigar (just load qname), it doesn't happen.

Any suggestions?  Right now I'm backing into it with a python script to strip out the cigar and MD tags instead, but prefer to just work in R.

Thanks,

Winston Timp

traceback output:

 traceback()
 8: stop(conditionMessage(err), "\n  file: ", path(file), "\n  index: ",
        index(file))
 7: value[[3L]](cond)
 6: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 5: tryCatchList(expr, classes, parentenv, handlers)
 4: tryCatch({
        .Call(func, .extptr(file), space, flag, simpleCigar, ...)
    }, error = function(err) {
        stop(conditionMessage(err), "\n  file: ", path(file), "\n  index: ",
            index(file))
    })
 3: .io_bam(.scan_bamfile, file, reverseComplement, yieldSize(file),
        tmpl, obeyQname(file), asMates(file), param = param)
 2: scanBam(z, param = param)
 1: scanBam(z, param = param)
 >


sessionInfo output:

 sessionInfo()
 R version 3.1.1 (2014-07-10)
 Platform: x86_64-pc-linux-gnu (64-bit)

 locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

 attached base packages:
 [1] parallel  stats     graphics  grDevices utils     datasets  methods
 [8] base

 other attached packages:
  [1] stringr_0.6.2           mgcv_1.8-3              nlme_3.1-118
  [4] hexbin_1.27.0           xtable_1.7-4            plyr_1.8.1
  [7] reshape2_1.4            ggplot2_1.0.0           ShortRead_1.22.0
 [10] GenomicAlignments_1.0.6 BSgenome_1.32.0         Rsamtools_1.16.1
 [13] GenomicRanges_1.16.4    GenomeInfoDb_1.0.2      BiocParallel_0.6.1
 [16] Biostrings_2.32.1       XVector_0.4.0           IRanges_1.22.10
 [19] BiocGenerics_0.10.0     knitr_1.7

 loaded via a namespace (and not attached):
  [1] base64enc_0.1-2     BatchJobs_1.4       BBmisc_1.7
  [4] Biobase_2.24.0      bitops_1.0-6        brew_1.0-6
  [7] checkmate_1.5.0     codetools_0.2-9     colorspace_1.2-4
 [10] compiler_3.1.1      DBI_0.3.1           digest_0.6.4
 [13] evaluate_0.5.5      fail_1.2            foreach_1.4.2
 [16] formatR_1.0         grid_3.1.1          gtable_0.1.2
 [19] highr_0.3           hwriter_1.3.2       iterators_1.0.7
 [22] labeling_0.3        lattice_0.20-29     latticeExtra_0.6-26
 [25] MASS_7.3-35         Matrix_1.1-4        munsell_0.4.2
 [28] proto_0.3-10        RColorBrewer_1.0-5  Rcpp_0.11.3
 [31] RSQLite_0.11.4      scales_0.2.4        sendmailR_1.2-1
 [34] stats4_3.1.1        tools_3.1.1         zlibbioc_1.10.0
 >

Thanks for the reproducible example. The problem was that the cigar was longer than a fixed size (32768 characters), and Rsamtools was failing badly. The cigar can now (1.18.1 in release available around noon on Friday via biocLite(), check the landing page, 1.19.2 in devel)  be any size.