[BioC] Bug in GenomicRanges precede/follow

[a.statham at garvan.org.au]

Hi, 

I just ran into this bug using the GRanges method of nearest 
(which calls precede & follow) with ignore.strand=TRUE

> nearest(GRanges("chr1", IRanges(1, width=1)), 
GRanges("chr1", IRanges(10, width=1)), ignore.strand=TRUE)
Error in strand(x) <- strand(subject) <- "+" : object 'x' not 
found


And tracked it down to here

> GenomicRanges:::.findPrecedeFollow_GRanges
function (query, subject, select, ignore.strand, where = 
c("precede", 
    "follow")) 
{
    leftOf <- "precede" == match.arg(where)
    if (ignore.strand) 
        strand(x) <- strand(subject) <- "+"

strand(x) should be strand(query)

> sessionInfo()
R version 2.15.0 (2012-03-30)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8    
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] xtable_1.7-0                       
BSgenome.Hsapiens.UCSC.hg19_1.3.17
 [3] BSgenome_1.24.0                    Biostrings_2.24.1                 
 [5] multicore_0.1-7                    rtracklayer_1.16.3                
 [7] Repitools_1.2.0                    GenomicRanges_1.8.7               
 [9] IRanges_1.14.4                     BiocGenerics_0.2.0                
[11] limma_3.12.1                      

loaded via a namespace (and not attached):
[1] bitops_1.0-4.1  RCurl_1.91-1    Rsamtools_1.8.5 
stats4_2.15.0  
[5] tcltk_2.15.0    tools_2.15.0    XML_3.9-4       
zlibbioc_1.2.0 


Thanks, 
Aaron

---
Aaron Statham
Postgraduate Scholar, Cancer Epigenetics
Garvan Institute of Medical Research   Tel: (02) 9295 8386
384 Victoria St Darlinghurst 2010   Fax: (02) 9825 8316
NSW Australia         email: a.statham at garvan.org.au