Jan Gleixner

ambiguity of `1./a` (real literal and infixOp)

6

#### Summary: `1./a` is parsed as `1.0/a` instead of `1 ./ a` (where are a is a `vector`). This confused me a bit. -------------------------- To avoid this ambiguity I would...

trimLRPatterns with indels not trimming as intended in case of net insertions or deletions between subject and pattern?

2

In the following examples I'd expect `trimLRPatterns` to always leave `ATCG`: ``` r library(Biostrings) subject DNAStringSet object of length 1: #> width seq #> [1] 4 ATCG trimLRPatterns(subject = subject,...

consensusString and consensusMatrix error for legth-0 input

1

Currently, `consensusString` fails for length-0 inputs: ``` r Biostrings::consensusString(character(0)) #> Error in h(simpleError(msg, call)): error in evaluating the argument 'x' in selecting a method for function 'consensusString': 'x' has no...

visualizemap does not indicate overhangs

1

```python from queen import * fragment = QUEEN(seq="CCGGTATGCG----/----ATACGCAGCT") fragment.printsequence(display=True) fig = visualizemap(fragment, seq= True ) fig = visualizemap(fragment, seq=True, rcseq = True) ```  I'd expect overhang bases to be...

specify minimal libcurl version as SystemRequirement

1

`rtracklayer` uses [CURLINFO_ACTIVESOCKET](https://curl.se/libcurl/c/CURLINFO_ACTIVESOCKET.html) (Added in curl 7.45.0 ) and [CURLINFO_CONTENT_LENGTH_DOWNLOAD_T](https://curl.se/libcurl/c/CURLINFO_CONTENT_LENGTH_DOWNLOAD_T.html) (Added in curl 7.55.0 ). Centos 7's (EOL was just a month ago) comes with libcurl/7.29.0. Instead of only conditionally...

Specify BLAS dependency in Makevars.win fixes #3 (``C:\RBuildTools\4.3\x86_64-w64-mingw32.static.posix\bin/ld.exe: sampling_functions.o:sampling_functions.cpp:(.text+0x2a20): undefined reference to `ddot_'``) See https://cran.r-project.org/doc/manuals/R-exts.html#Using-Makevars