Manuel Holtgrewe

Inline

1

I have a problem with the `inlineslides` slide builder (both with the latest release and when building directly from Githbub). Please advice. ``` # sphinx-build -b inlineslides -d build/doctrees source...

Hi, we have the same problem as described in #3. `bbcp` is a very useful tool for us but ownership is not preserved. The UID on the source does not...

Status of conda package?

2

Hi, I'm interested in having misopy in bioconda. I realize there already is a "conda" sub folder. What's the status of conda packaging?

Median and median-absolute-deviation results

1

Would it be possible to add these statistics? They are generally more stable than mean and stddev...

See http://gatkforums.broadinstitute.org/discussion/1204/what-input-files-does-the-gatk-accept-require for the format description.

Adding functions for obtaining file size and approximate position in file.

2

I would like to add the following feature to the `VirtualStream` class and also expose this functionality in the `FormattedFile` class. - `Size::Type fileSize(TFile const & file);` returns the file...

One end anchored reads not written out correctly in FragmentStore SAM Output

1

From Trac, @weese is this still an issue? In the case of paired reads where one mate aligns and the other does not, the SAM output of the FragmentStore is...

Add soft/hard clipping support to FragmentStore

4

The FragmentStore does neither support soft nor hard clipping. For soft-clipping, the full sequence is in the SEQ field of SAM files and the anchor gaps data structure supports clipping...

Rename hash2, hash2Next, hashUpper, hash2Upper

6

The names of the functions hash2, hash2Next, hashUpper and hash2Upper are not clear enough to get the idea immediately. As far as I understand, the function hash2 forces the computation...

Add align_profile module

1

We need some means to align sequences against profiles. Here is some code: ​https://github.com/holtgrewe/align_profile