[BioC] readPileup() Error

Ron Ophir ron at volcani.agri.gov.il
Thu Nov 10 09:10:49 CET 2011

Dear BMMs,

The session information is listed below.
When I read a pileup file (readPileup) I got as an output of samtools
0.1.18, I get the following error

Snp = readPileup(pileupFile,variant="SNP")

Error in scan(file, what, nmax, sep, dec, quote, skip, nlines,
na.strings,  : 
  scan() expected 'an integer', got '^<,'


The pileup format in the example of readPileup() function is

6	33701	A	G	21	21	12	35

The pileup format at samtools web pages is 

seq1 272 T 24  ,.$.....,,.,.,...,,,.,..^+. <<<+;<<<<<<<<<<<=<;<;7<&

and in my pileup is

Cs1,6RhaT	332	A	9	,,,..^;,^E,^Z.^Z.

It seems to me that the error is obvious, however I don't know whether
it is a bug or a feature. If it is a feature how to run readPileup
correctly to be able reading latest pileup format?



BMM bioconductor mailing-list member

R version 2.14.0 (2011-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=C                LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           

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

other attached packages:
[1] Rsamtools_1.6.1     Biostrings_2.22.0   GenomicRanges_1.6.2
[4] IRanges_1.12.1     

loaded via a namespace (and not attached):
[1] bitops_1.0-4.1     BSgenome_1.22.0    RCurl_1.7-0
[5] tools_2.14.0       XML_3.4-3          zlibbioc_1.0.0

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