[BioC] package Genominator with ShortRead-annotation question

[nitzan kol [guest]]

in the simple annotation objects chr entries should be the original chr numbers or indices into chrMap?
in your withShortRead example THRO55C.1 had VIII translated to 8 in the simple annotation form when in chrMap it has location 13 in chrMap.

 thank you
Nitzan

 -- output of sessionInfo(): 

R version 2.11.0 (2010-04-22) 
x86_64-unknown-linux-gnu 

locale:
 [1] LC_CTYPE=en_US.iso885915       LC_NUMERIC=C                  
 [3] LC_TIME=en_US.iso885915        LC_COLLATE=en_US.iso885915    
 [5] LC_MONETARY=C                  LC_MESSAGES=en_US.iso885915   
 [7] LC_PAPER=en_US.iso885915       LC_NAME=C                     
 [9] LC_ADDRESS=C                   LC_TELEPHONE=C                
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C           

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

other attached packages:
 [1] Genominator_1.2.0   GenomeGraphs_1.8.0  biomaRt_2.4.0      
 [4] RSQLite_0.9-1       DBI_0.2-5           ShortRead_1.6.2    
 [7] Rsamtools_1.0.8     lattice_0.18-5      Biostrings_2.16.9  
[10] GenomicRanges_1.0.9 IRanges_1.6.17     

loaded via a namespace (and not attached):
[1] Biobase_2.8.0 hwriter_1.3   RCurl_1.6-10  tools_2.11.0  XML_3.4-3

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