Martin Morgan

handle multiple calls to scanBam() on an open BamFile

2

https://github.com/LTLA/csaw/pull/4#issuecomment-480141778 and https://support.bioconductor.org/p/119631 ``` > fl = system.file(package="Rsamtools", "extdata", "ex1.bam") > header = scanBamHeader(fl)[[1]]$targets > bf = open(BamFile(fl)) > which = GRanges(paste0(names(header), ":", 1, "-", header)) > length(scanBam(bf, param =...

To make the repository more consistent with Rule 9 of https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854 Additionally, add github magic so that new issues create an appropriate template for contributing FAIRly.

Table 2 of https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007854 suggests metadata to describe resources and facilitate FAIR sharing of training material. These can be included as DESCRIPTION dcf ('debian control format') fields

RELEASE_3_12 failures on Windows means that 1.50.0 is not propagating

1

http://bioconductor.org/checkResults/release/bioc-LATEST/rtracklayer/tokay1-checksrc.html reflected in https://support.bioconductor.org/p/p133891/

search not working

4

I don't think search is working on https://bioconductor.org/ ? I just get a message about a timeout or invalid search term..., e.g., https://bioconductor.org/help/search/index.html?search-bar=rsamtools/ returns > A timeout or invalid search...

mapIds(..., multiVal="asNA") returns logical() instead of character() when all ids map multiply

6

``` > class(mapIds(EnsDb.Hsapiens.v86, "BCL2", "TXID", "GENENAME", multiVals="asNA")) [1] "logical" ```

`subset()` fails with zero-dimension objects and missing values

1

Compare ``` > subset(DataFrame()) Error: subscript is a logical vector with out-of-bounds TRUE values > subset(data.frame()) data frame with 0 columns and 0 rows ``` This is because https://github.com/Bioconductor/S4Vectors/blob/b14a989db670382566500d025e49e15fbf46ac12/R/eval-utils.R#L47 returns...