Dear Bioc developers, There seems to be an issue with GenomicAlignments or dependent packages as I can no longer read BAM files with readGAlignmentPairs that could be read without problems previously (see example below). I assume this is a general problem but can provide test files if necessary. Leonard
readGAlignmentPairs(file)
Error in .Call2("Integer_explode_bits", x, bitpos, PACKAGE = "S4Vectors") :
'bitpos' must contain values >= 1
sessionInfo()
R Under development (unstable) (2014-11-04 r66932) Platform: x86_64-unknown-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] stats4 parallel stats graphics grDevices utils datasets [8] methods base other attached packages: [1] GenomicAlignments_1.3.14 Rsamtools_1.19.14 Biostrings_2.35.6 [4] XVector_0.7.3 GenomicRanges_1.19.21 GenomeInfoDb_1.3.7 [7] IRanges_2.1.32 S4Vectors_0.5.14 BiocGenerics_0.13.3 loaded via a namespace (and not attached): [1] base64enc_0.1-2 BatchJobs_1.5 BBmisc_1.8 BiocParallel_1.1.9 [5] bitops_1.0-6 brew_1.0-6 checkmate_1.5.0 codetools_0.2-9 [9] DBI_0.3.1 digest_0.6.6 fail_1.2 foreach_1.4.2 [13] iterators_1.0.7 RSQLite_1.0.0 sendmailR_1.2-1 stringr_0.6.2 [17] tools_3.2.0 zlibbioc_1.13.0