Hi Craig,
Sorry for taking so long to answer this. Yes some tools seem to generate
SAM/BAM output with zero-length operations in the CIGAR field
and the official SAM Format Spec 0.1.2-draft apparently have no
problem with that:
http://samtools.sourceforge.net/SAM1.pdf
( see regular expression for the CIGAR string: ([0-9]+[MIDNSHP])+|\* )
I've modified the CIGAR handling code in GenomicRanges for
allowing zero-length operations in CIGAR strings.
This will be available via biocLite() in the next 24 hours in
GenomicRanges 1.0.5 (release) and GenomicRanges 1.1.15 (devel).
Cheers,
H.
On 05/27/2010 03:29 PM, Craig Johnson wrote:
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
_______________________________________________
Bioc-sig-sequencing mailing list
[email protected]
https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
