I have two BAM files generated from ABI's Bioscope aligner that I want to import using readBamGappedAlignments(). One of the files imports without issue but the second gives me this error:
Error in cigarToIRangesListByAlignment(x...@cigar, x...@start) : in 'cigar' element 3315124: invalid CIGAR operation length at char 5 The cigar at line 3315124 of the SAM file is 9M0N32M9H Can anyone suggest what causes this error? I have reads earlier in the SAM/BAM file that have 'ON' in them so even though I don't know what 'ON' means that doesn't seem to be the issue. > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-unknown-linux-gnu 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=C 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] stats graphics grDevices utils datasets methods base other attached packages: [1] org.Hs.eg.db_2.4.1 RSQLite_0.9-0 DBI_0.2-5 [4] AnnotationDbi_1.10.1 Biobase_2.8.0 rtracklayer_1.8.1 [7] RCurl_1.4-2 bitops_1.0-4.1 GenomicFeatures_1.0.0 [10] Rsamtools_1.0.1 Biostrings_2.16.0 GenomicRanges_1.0.1 [13] IRanges_1.6.2 loaded via a namespace (and not attached): [1] biomaRt_2.4.0 BSgenome_1.16.1 tools_2.11.0 XML_3.1-0 Thank you, Craig ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
