[BioC] [devteam-bioc] GenomicRanges::findOverlap unexpected behaviour with 0 width ranges

[Valerie Obenchain]

Hello,

Thanks for reporting the bug. The behavior is fixed in IRanges 1.19.38 
and 1.18.4.

A zero-width range in 'query' no longer registers as a hit, regardless 
of 'maxgap' and 'minoverlap' values.

 > findOverlaps(rangeZero, rangeContains, maxgap=1) # match
Hits of length 0
queryLength: 1
subjectLength: 1

 > findOverlaps(rangeZero, rangeStartMatch, maxgap=1) # match
Hits of length 0
queryLength: 1
subjectLength: 1


Valerie

On 09/19/2013 10:54 PM, Maintainer wrote:
>
> The hits returned when using findOverlap seem strange when a zero width range is involved. By default, findOverlap does not return any hits with a zero width range, even if other range contains the zero width range. Presumably this is due the requirement of a positive, non-zero minoverlap. If a maxgap is set, a hit is returned only if the zero width range is the query.
>
> According to the documentation, "all matches must additionally satisfy the minoverlap constraint". This constraint is violated when a zero-width range is passed as the query parameter with a non-zero maxgap. I presume this is a bug, is it not?
>
> rangeZero <- IRanges(5, 4)
> rangeContains <- IRanges(3, 6)
> rangeStartMatch <- IRanges(5, 5)
> findOverlaps(rangeZero, rangeContains) # no match
> findOverlaps(rangeZero, rangeStartMatch) # no match
> findOverlaps(rangeContains, rangeZero) # no match
> findOverlaps(rangeStartMatch, rangeZero) # no match
> findOverlaps(rangeZero, rangeContains, maxgap=1) # match
> findOverlaps(rangeZero, rangeStartMatch, maxgap=1) # match
> findOverlaps(rangeContains, rangeZero, maxgap=1) # no match
> findOverlaps(rangeStartMatch, rangeZero, maxgap=1) # no match
>
>
>   -- output of sessionInfo():
>
>
>
> R version 3.0.1 (2013-05-16)
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_Australia.1252  LC_CTYPE=English_Australia.1252    LC_MONETARY=English_Australia.1252 LC_NUMERIC=C
> [5] LC_TIME=English_Australia.1252
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] GenomicFeatures_1.12.3 AnnotationDbi_1.22.6   Biobase_2.20.1         GenomicRanges_1.12.5   IRanges_1.18.3         BiocGenerics_0.6.0
> [7] BiocInstaller_1.10.3
>
> loaded via a namespace (and not attached):
>   [1] biomaRt_2.16.0     Biostrings_2.28.0  bitops_1.0-6       BSgenome_1.28.0    DBI_0.2-7          RCurl_1.95-4.1     Rsamtools_1.12.4   RSQLite_0.11.4
>   [9] rtracklayer_1.20.4 stats4_3.0.1       tools_3.0.1        XML_3.98-1.1       zlibbioc_1.6.0
>
> --
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>
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