[Bioc-devel] [devteam-bioc] Error in findOverlaps

[Ou, Jianhong]

Dear Hervé,

Is it possible to ignore minoverlap when people set maxgap greater than 0
and give a message for that?

Yours sincerely,

Jianhong Ou

LRB 670A
Program in Gene Function and Expression
364 Plantation Street Worcester,
MA 01605




On 7/23/13 5:35 PM, "Hervé Pagès" <hpages at fhcrc.org> wrote:

>Hi,
>
>This fails in Bioc-devel only and the following fix "seems" to address
>the problem:
>
>   hpages at thinkpad:~/svn/bioconductor/Rpacks/IRanges$ svn diff
>R/findOverlaps-methods.R
>   Index: R/findOverlaps-methods.R
>   ===================================================================
>   --- R/findOverlaps-methods.R	(revision 78801)
>   +++ R/findOverlaps-methods.R	(working copy)
>   @@ -142,7 +142,7 @@
>                # preprocess query
>                preprocRes <- .preProcess_findOverlaps_query(query,
>maxgap, minoverlap)
>                origQuery <- preprocRes$origQuery
>   -            unsortedQuery <- preprocRes$origQuery
>   +            unsortedQuery <- preprocRes$unsortedQuery
>                query <- preprocRes$query
>                query_ord <- preprocRes$query_ord
>
>However a *real* fix would be to actually clarify what's the meaning of
>using 'maxgap' and 'minoverlap' together. Right now the result below
>doesn't make much sense to me (using Bioc-release):
>
>   > findOverlaps(IRanges(1, 5), IRanges(7, 10), maxgap=3, minoverlap=2)
>   Hits of length 0
>   queryLength: 1
>   subjectLength: 1
>
>   > findOverlaps(IRanges(1, 5), IRanges(7, 10), maxgap=4, minoverlap=2)
>   Hits of length 1
>   queryLength: 1
>   subjectLength: 1
>     queryHits subjectHits
>      <integer>   <integer>
>    1         1           1
>
>H.
>
>
>On 07/23/2013 12:08 PM, Maintainer wrote:
>> Hi,
>>
>> I got "negative widths are not allowed" error when I use findOverlaps.
>> Could anybody help me to figure this out? Thanks. Here is the code:
>>
>>  > library("IRanges")
>> Loading required package: BiocGenerics
>> Loading required package: parallel
>>
>> Attaching package: ŒBiocGenerics¹
>>
>> The following objects are masked from Œpackage:parallel¹:
>>
>>      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
>>      clusterExport, clusterMap, parApply, parCapply, parLapply,
>>      parLapplyLB, parRapply, parSapply, parSapplyLB
>>
>> The following object is masked from Œpackage:stats¹:
>>
>>      xtabs
>>
>> The following objects are masked from Œpackage:base¹:
>>
>>      anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
>>      duplicated, eval, Filter, Find, get, intersect, lapply, Map,
>>      mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
>>      Position, rank, rbind, Reduce, rep.int, rownames, sapply, setdiff,
>>      sort, table, tapply, union, unique, unlist
>>
>>  > Ranges1 <- sort(IRanges(start=c(3123260, 167889600), end=c(3123360,
>> 167893599), names=c("Site5", "Site12")))
>>  > Ranges2 <- sort(IRanges(start=c(312326, 3123260, 167888600),
>> end=c(312586, 3123470, 167888999), names=c("t11", "t5", "t17")))
>>  > tree = IntervalTree(Ranges2)
>>  > findOverlaps(tree, query = Ranges1, maxgap = 1000, minoverlap = 20,
>> select = "first")
>> Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE =
>> "IRanges") :
>>    solving row 2: negative widths are not allowed
>>  > traceback()
>> 11: .Call(.NAME, ..., PACKAGE = PACKAGE)
>> 10: .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges")
>> 9: solveUserSEW0(start = start, end = end, width = width)
>> 8: IRanges(pmax.int(qstart, sstart), pmin.int(send, qend))
>> 7: .local(x, ...)
>> 6: ranges(result, unsortedQuery, subject)
>> 5: ranges(result, unsortedQuery, subject)
>> 4: .postProcess_findOverlaps_result(result, unsortedQuery, origQuery,
>>         subject, type, minoverlap, maxgap, origSelect)
>> 3: .local(query, subject, maxgap, minoverlap, type, select, ...)
>> 2: findOverlaps(tree, query = Ranges1, maxgap = 1000, minoverlap = 20,
>>         select = "first")
>> 1: findOverlaps(tree, query = Ranges1, maxgap = 1000, minoverlap = 20,
>>         select = "first")
>>  > sessionInfo()
>> R Under development (unstable) (2013-04-30 r62697)
>> Platform: x86_64-apple-darwin12.3.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> [8] base
>>
>> other attached packages:
>> [1] IRanges_1.19.19    BiocGenerics_0.7.3
>>
>> loaded via a namespace (and not attached):
>> [1] stats4_3.1.0
>>
>>
>> Yours sincerely,
>>
>> Jianhong Ou
>>
>> LRB 670A
>> Program in Gene Function and Expression
>> 364 Plantation Street Worcester,
>> MA 01605
>>
>>
>> ________________________________________________________________________
>> devteam-bioc mailing list
>> To unsubscribe from this mailing list send a blank email to
>> devteam-bioc-leave at lists.fhcrc.org
>> You can also unsubscribe or change your personal options at
>> https://lists.fhcrc.org/mailman/listinfo/devteam-bioc
>>
>
>-- 
>Hervé Pagès
>
>Program in Computational Biology
>Division of Public Health Sciences
>Fred Hutchinson Cancer Research Center
>1100 Fairview Ave. N, M1-B514
>P.O. Box 19024
>Seattle, WA 98109-1024
>
>E-mail: hpages at fhcrc.org
>Phone:  (206) 667-5791
>Fax:    (206) 667-1319