Luca Beltrame

RFE: SImilar options to trimmomatic's CROP

4

Sometimes I just want to trim "from xx bases onward" or "take just the first xx bases". In trimmomatic (considerably slower than atropos) this is obtained with the `HEADCROP` and...

Documentation: some more examples for common use cases (adding extra headers)

3

I'm opening this as an issue so it's tracked. In particular, it would be nice to have in the docs some indication on how to add extra headers for common...

FTBFS when using GCC 9

1

Found in openSUSE Tumbleweed when rebuilding rttr against GCC 9. ``` [ 170s] In file included from /home/abuild/rpmbuild/BUILD/rttr-0.9.6/src/rttr/../rttr/detail/registration/registration_impl.h:43, [ 170s] from /home/abuild/rpmbuild/BUILD/rttr-0.9.6/src/rttr/../rttr/registration.h:821, [ 170s] from /home/abuild/rpmbuild/BUILD/rttr-0.9.6/src/rttr/../rttr/registration:46, [ 170s] from /home/abuild/rpmbuild/BUILD/rttr-0.9.6/src/unit_tests/constructor/constructor_param_info_test.cpp:28:...

Use FeatureSummary instead of find_package(FOO REQUIRED)

7

`FeatureSummary` allows CMake to finish configuring and yet print out properly the dependencies that are missing, divided in optional and required. ```cmake include(FeatureSummary) find_package(FOO) # Note no REQUIRED set_package_properties(FOO TYPE...

Crash when attempting to import an OrgDb package from Bioconductor

8

Minimal reproducer, with R 4.0.2 and the latest Bioconductor (observed on openSUSE Tumbleweed): ``` In [1]: from rpy2.robjects.packages import importr In [2]: importr("org.Hs.eg.db") R[write to console]: Error in as.character(sys.call(sys.parent())[[1L]]) :...

Document the purpose of each open port

2

This is important for those who run this service along others (potential port conflicts). In particular, what needs to be known if any of these need to be actually exposed....

Allow changing sample names

4

I'm filing this issue because despite the plethora of VCF reading/writing libraries for Python, no one of them implements this. (I filed a similar request for pysam).

lollipopPlot2 and lollipopPlot parse protein variants differently

3

**Describe the issue** As an example: - R1443* in BRCA1 is correctly plotted by lollipopPlot - R1443* is *discarded* by `get_lp_data` invoked by lollipopPlot2 This also happens with HGVSp notation,...

readGistic: possible parsing errors in case there is a single significant peak

5

I have a GISTIC result where only one significant peak was found. When reading the GISTIC file, the parsing gets likely confused, because a number of warnings are written: ```...

RFE: Allow subsetting samples in the GISTIC class

3

As the issue subject says, it might be useful to subset samples in GISTIC objects, similar to what it is done for MAFs. A use case I have is a...