Re: [Bioc-devel] MRD measurements in Leukemic patients using NGS data in r

something like this perhaps? library(Rsamtools) BamFiles <- BamFileList(lapply(list.files(pattern=".bam$"), BamFile)) names(BamFiles) <- sapply(strsplit(list.files(pattern=".bam$"), "\\."), `[`, 1) show(BamFiles) #BamFileList of length 14 #names(14): Normal_0813_S19_R1_001 Normal_2013_S18_R1_001

Re: [Bioc-devel] Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased)

Hi, If you can replicate the latex/knitr/sweave issue locally, try installing Biostrings from my GitHub fork used in the PR. This should solve the issue, if it is about the ellipsis character causing problems on windows only. If it doesn't, it probably has more to do with the way unicode

Re: [Bioc-devel] MRD measurements in Leukemic patients using NGS data in r

Dear Tim, I installed Rsamtools and ran it on a bamfile using the following command to get nucleotide count for 2 hotspot regions. library(Rsamtools) bamfile <- "test.bam" bf <- BamFile(bamfile) param <- ScanBamParam(which=GRanges(c("4", "9"), IRanges(start=c(55599321, 5073770),

Re: [Bioc-devel] Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased)

you are not wrong ... thanks for pointing this out https://github.com/Bioconductor/Biostrings/pull/33 On Sat, Mar 7, 2020 at 2:33 PM Shepherd, Lori wrote: > I could be wrong but I think there is an open issue and PR already > submitted that might be related. > > Get Outlook for Android

Re: [Bioc-devel] Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased)

I could be wrong but I think there is an open issue and PR already submitted that might be related. Get Outlook for Android From: Bioc-devel on behalf of Vincent Carey Sent: Saturday, March 7, 2020 12:58:57 PM To: Ulrich Bodenhofer Cc:

Re: [Bioc-devel] Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased)

I have a feeling that the best way to get action here will be to file an issue and perhaps a PR at https://github.com/Bioconductor/Biostrings On Sat, Mar 7, 2020 at 7:12 AM Ulrich Bodenhofer wrote: > Dear colleagues, > > As noted in my previous message, I have encountered problems with the >

[Bioc-devel] Biostrings: unicode character ("compact ellipsis") in print()/show() output (2nd attempt, rephrased)

Dear colleagues, As noted in my previous message, I have encountered problems with the new way of displaying sequences/sequence sets that now use a UTF-8 ellipsis character (internally defined as R object 'compact_ellipsis' in the package) when the output is included in a LaTeX document