Dear list, 

I have been trying to use seqmentSeq package. Running the examples in the package was successful, but on my data gives error at "readGeneric" function:

here is my test code and attached data files (was attached, but held for review because it is bigger than 40 KB).
libfiles <- c("V010.mapped_tt.txt","V010.mapped_tt2.txt")
libnames <- c( "tt1","tt2")
replicates <- c("fGS_OSS","fGS_OSS")
aD <- readGeneric(files = libfiles, dir = paste(datadir,"test/",sep=""), header = TRUE,
		replicates = replicates, libnames = libnames, 
		chrs = c("chr2L","chr2R"), chrlens = c(23011544,21146708),  gap = 100,polyLength = 10)


Reading files......done!
Analysing tags..........done!
Error in validObject(.Object) : 
  invalid class “GRanges” object: 'ranges' contains values outside of sequence bounds

debugging message:

Enter a frame number, or 0 to exit   

1: readGeneric(files = libfiles, dir = paste(datadir, "test/", sep = ""), head
2: .processTags(Tags, verbose = verbose, estimationType = estimationType, gap 
3: `seqinfo<-`(`*tmp*`, new2old = chrmatch, value = <S4 object of class "Seqin
4: `seqinfo<-`(`*tmp*`, new2old = chrmatch, value = <S4 object of class "Seqin
5: update(x, seqnames = makeNewSeqnames(x, new2old, seqlevels(value)), seqinfo
6: update(x, seqnames = makeNewSeqnames(x, new2old, seqlevels(value)), seqinfo
7: initialize(object, ...)
8: initialize(object, ...)
9: validObject(.Object)


> sessionInfo()
R version 2.14.0 (2011-10-31)
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=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] Rmpi_0.5-9          snow_0.3-7          segmentSeq_1.6.0   
 [4] ShortRead_1.12.0    latticeExtra_0.6-19 RColorBrewer_1.0-5 
 [7] Rsamtools_1.6.1     lattice_0.20-0      GenomicRanges_1.6.3
[10] baySeq_1.8.0        ggplot2_0.8.9       proto_0.3-9.2      
[13] reshape_0.8.4       plyr_1.6            limma_3.10.0       
[16] Biostrings_2.22.0   IRanges_1.12.1     

loaded via a namespace (and not attached):
[1] Biobase_2.14.0     bitops_1.0-4.1     BSgenome_1.22.0    hwriter_1.3       
[5] RCurl_1.7-0        rtracklayer_1.14.3 tools_2.14.0       XML_3.4-3         
[9] zlibbioc_1.0.0    


Thank you very much for the help, 

Jean
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