See #2700 for background, cross reference biopython/biopython#2833 (comment) e.g.

$ grep assertTrue *.py | grep "=="
common_BioSQL.py:        self.assertTrue(self.db.load(seqiter) == 1)
test_ClustalOmega_tool.py:        self.assertTrue(error.strip() == "" or
...

and:

$ grep assertFalse *.py | grep "!="
test_Restriction.py:        self

From @agitter in #986

Tracking the contribution types in the metadata file makes sense to me. Should we save v2 author ordering and mouseover contributions for a follow up issues/pull request?

I am planning a large alignment run on a non human species using a non alt aware reference.
I would like to determine which combination of BWA MEM "-M" and "-Y" options I should be using.
As far as I can tell "-M" used to be needed for the Picard compatibility as sometimes mentioned in the man page.

GATK 4 now recommends not to use "-M" for the human alt aware reference.
But they are now rec

Three very minor typos are present in these documents that break the code when copied-and-pasted as they are.

Link: https://gatk.broadinstitute.org/hc/en-us/community/posts/360056484652-Typos-in-docs

--

1.  https://gatk.broadinstitute.org/hc/en-us/articles/360036726571-LeftAlignAndTrimVariants

the fifth code block on this page

This would make the process for making small corrections easier for non-developers. From a comment on #8349.

This should be pretty easy to do and a good task for a new developer or community member looking to make a small contribution.

As part of the process of bringing vg into debian's package system, I'd like to develop more extensive documentation of vg and its subcommands. This tool is increasingly used by people who are outside of the core group of developers, and they face a steep learning curve to understand what the various systems do.

I suggest we develop per-command documentation. These could begin in the form of ma

I tried to run Hail with Spark 2.4.4 built for Scala 2.12, and it did not work. It does work with Spark 2.4.4 built for Scala 2.11.

Here's the error I got with Scala 2.12:

Py4JJavaError: An error occurred while calling z:is.hail.HailContext.apply.
: java.lang.NoSuchMethodError: scala/Predef$.refArrayOps([Ljava/lang/Object;)Lscala/collection/mutable/ArrayOps; (loaded from file:/home/hammer

Dear @kblin,

I would like to use ncbi-gneome-download as a python module within my pipeline and I have been having problems to decipher the arguments to pass to the download call. I guess the readme and documentation is not up to date or I am missing something.

For example, I tried on the command line and it worked fine for me the following code:

ncbi-genome-download -s genbank -F fast

• Search whether this issue (or a similar issue) has been solved before
  using the search tab above. Link the previous issue if appropriate below.

• Paste your deepTools version (deeptools --version) and your python
  version (python --version) below.
  deeptools 3.3.2
  Python 3.6.0

• Paste the full deepTools command that produces the issue below
  (ignore if you simply sp

Documentation for wcFst says:

"Output : 3 columns :
1. seqid
2. position
3. target allele frequency
4. background allele frequency
5. wcFst"

In reality, the output is 3 columns: 1, 2, and 5.

This discrepancy seems to affect segmentFst, which returns an error "FATAL: not valid wcFst input"

What's the intended meaning of PDBHeader.getDescription? It is populated in mmCIF with the _struct_keywords.pdbx_keywords field, the same as getClassification() (e.g. lyase, oxidase, etc). It seems to be unused in PDB files. It's also modified in a couple places for partial structures, e.g. "subset of 1ABC".

There's an emerging standard for adding CITATION files to the root of a project to encourage academic citations.

We should add one to JB1.

Format spec: https://citation-file-format.github.io/

The test script shows 2 warnings in the log. You can see the Travis log.

$ perl -cw scripts/test/simple_tests.pl 
\1 better written as $1 at scripts/test/simple_tests.pl line 4671.
\1 better written as $1 at scripts/test/simple_tests.pl line 4672.
scripts/test/simple_tests.pl syntax OK

This part.

scripts

The current documentation README is starting to become unwieldy, and it would be nice to have an auto-documented API using Sphinx. A few things to do:

• explain variant types and filters for FastaVariant (#129)
  ...

Hi there,

On this page (http://kundajelab.github.io/dragonn/cloud_resources.html), the step "Alternatively, you can run the Dragonn jupyter notebook by executing the following commands: sudo su passwd ubuntu enter your desired password when prompted." suggests that
sudo su passwd ubuntu is a one line command. For whatever reason, this step only worked when I separated sudo su and `pass

It would be helpful to have a complete list of all standard Python modules and a guide as to which ones are supported, in progress, going to be supported, or not going to be supported ever. For example, is the threading module ever going to be supported? Will threading be handled with Seq's pipelines only? Will the multiprocessing module be supported?

Having this list will encourage people t

The current implementation of slice md5 validation proceeds in two steps; it first tries to validate the md5 for the entire slice span. If that fails, it falls back to checking the md5 for a smaller span ([terminating one base earlier](https://github.com/