evanbiederstedt

What are the statistics affected by `alfred qc --bed`?

2

Hi Tobias I haven't dug closely into the source code for this, so apologies if this question is a bit lazy: What are the metrics affects by using the optional...

Code snippet from "Listing 5.6 Inspecting endianness". These should either be comments or removed entirely----they don't exist in the publication "Rust In Action" CC @timClicks

This is the code snippet for "Listing 5.4 How u16 bit patterns translate to a fixed number of integers". Although this is what the book has, this code will not...

Feature request: overriding `Reference genome mismatch` error

2

Hello This issue is related to the following: https://github.com/Illumina/manta/issues/93 I'm configuring Manta as follows (and the bug is the same for germline or TN pairs) ``` configManta.py \ --referenceFasta file.fa...

Hi @cjain7 Thanks for the excellent tool! A small request: could you include small example files such that users could quickly check that the installation was successful? This should also...

brew installation, update documentation

1

Hi there Low priority request: https://bedtools.readthedocs.io/en/latest/content/installation.html ``` brew tap homebrew/science brew install bedtools ``` It looks like `brew tap homebrew/science` is no longer functional: ``` $ brew tap homebrew/science Error:...

"Parameter required for id", resolved by manually inserting id fields in `-sr` arguments

1

Previous issues have dealt with the error "Parameter required for id" with respect to Lumpy: https://github.com/arq5x/lumpy-sv/issues/82) For this case, previously resolutions will not solve this issue, i.e. (1) the BAMs...

Feature request: integrating with Travis-CI

2

Hi there Thanks for the great tool! I've been testing an R package with C++ bindings, and it's useful for CRAN submissions to understand how the package builds on the...

Hi Heng Li It might be good to update the README with respect to downloading C. elegans The following doesn't work: ``` $ fastq-dump --split-spot SRR065390.lite.sra fastq-dump.2.8.1 err: item not...

Cython compilation errors, 'CompileError: command 'gcc' failed with exit status 1\n'

4

I've installed the package with python 2.7.14 as recommend. Using `gcc (GCC) 6.2.0` ``` Processing /path/location/NucleoATAC Requirement already satisfied (use --upgrade to upgrade): NucleoATAC==0.3.2 from file://path/location/NucleoATAC in /path/python-2.7.14/lib/python2.7/site-packages Requirement already...