[Bioc-sig-seq] readBamGappedAlignments() cigar error

[Craig Johnson]

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 at cigar, x at 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

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