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 -- Sent via the guest posting facility at bioconductor.org.

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 > > -- > Sent via the guest posting facility at bioconductor.org. > > ____________________________________________________________________ ____ > 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 >