Hello,

I am getting no matches using locateVariants, while I would expect some.
Here is one example:

gr= GRanges(seqnames=Rle('chr12'), ranges= IRanges(33804059, 33804059))
txdb= TxDb.Mmusculus.UCSC.mm9.knownGene
length(locateVariants(query= gr, subject= txdb, region=AllVariants()))
[1] 0
Warning message:
In `start<-`(`*tmp*`, value = c(4795974L, 4795974L, 4845775L, 4845775L,  :
  trimmed start values to be positive

(by the way, I also do not understand what this warning message is
referring to)


while I would expect a match to this TxDb entry:

transcripts(txdb)[10888]
GRanges with 1 range and 2 metadata columns:
      seqnames               ranges strand |     tx_id     tx_name
         <Rle>            <IRanges>  <Rle> | <integer> <character>
  [1]    chr12 [33796576, 33832451]      - |     38273  uc007nil.1
  ---
  seqlengths:
           chr1         chr2         chr3 ...  chrY_random chrUn_random
      197195432    181748087    159599783 ...     58682461      5900358


thanks for any help on this, I hope it has not been asked before,

mattia


sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:
[1] C/UTF-8/C/C/C/C

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

other attached packages:
 [1] TxDb.Mmusculus.UCSC.mm9.knownGene_2.10.1
 [2] GenomicFeatures_1.14.2
 [3] AnnotationDbi_1.24.0
 [4] Biobase_2.22.0
 [5] VariantAnnotation_1.8.6
 [6] Rsamtools_1.14.2
 [7] Biostrings_2.30.1
 [8] GenomicRanges_1.14.3
 [9] XVector_0.2.0
[10] IRanges_1.20.6
[11] BiocGenerics_0.8.0

loaded via a namespace (and not attached):
 [1] BSgenome_1.30.0    DBI_0.2-7          RCurl_1.95-4.1
RSQLite_0.11.4
 [5] XML_3.95-0.2       biomaRt_2.18.0     bitops_1.0-6
rtracklayer_1.22.0
 [9] stats4_3.0.2       tools_3.0.2        zlibbioc_1.8.0

	[[alternative HTML version deleted]]

