darrin t schultz

To make this a little more friendly to those not familiar with `bash`, maybe change the formatting of rm -rf staging python stageflowcells.py data basecalls staging read_fast5_basecaller.py -r -i staging/$flowcell...

make fails for 2.2.10

3

fails on ubuntu 16.04 LTS. Log is attached below. See #119 [2.2.10.makefail.txt](https://github.com/gmarcais/Jellyfish/files/1996094/2.2.10.makefail.txt)

Add arithmetic meanqual

1

I added a function that calculates the arithmetic mean of the quality scores, rather than the geometric mean as `meanqual` currently does. For motivation, please see [this blog post](https://gigabaseorgigabyte.wordpress.com/2017/06/26/averaging-basecall-quality-scores-the-right-way/). Using...

cooler balance drops many interactions

2

I have a cool file that appears to be fine - there are reads in pretty much every bin. Here it is as a ginteractions file: ``` NC_042997.1 0 1000000...

Hi, this warning is a bit vague. What do you think about making it say something like "output directory already exists, so quitting to avoid overwriting files." Or if there...

multivec only displaying one track, only allowing two track types

5

_Commit_: I installed `higlass-manage` on Ubuntu 20.04.4. Typing `higlass-manage version` shows `0.8.0`. I am not sure what version of `higlass` is running inside the docker. #### Steps to reproduce 1....

Update falconsense.C

2

flushes the falconsense buffer when working on a new read so that it will be easier to determine which reads are causing falconsense to slow down. addresses #1202 partly

[Exception: Call 'which samtools' returned 256] on install

1

I'm trying to install FALCON via the `install_unzip.sh` script [found via readthedocs](https://pb-falcon.readthedocs.io/en/latest/quick_start.html). I'm trying to install here `/usr/local/bin/falcon-201805` with the command `sudo bash -ex install_unzip_180504.sh /usr/local/bin/falcon-201805`. However, I consistently get...

manpage -1 -2 options

2

the language in the manpage for -1 is a little confusing: "read11.fq,read12.fq,read13.fq" Can you consider changing it to something more explicit that will reflect how most people with use the...

Feature request: Allow gzipped fastq for collapse_isoforms_by_sam.py

1

Can you possibly add support for gzipped fastq and fasta files for `collapse_isoforms_by_sam.py`? It's a big difference in file size and it would be nice to be able to use...