Darek Kedra

[enhancement] stat for a region/list of regions

5

Hello, Would it be possible to implement simple median coverage stats for a selected region? While one can get the data using i.e. ```d4tools view input.bam 22:39349000-39349100``` there is "some...

BAM/BED to parquet

3

Hello, Would it be possible to provide a minimal example be it in Scala/python/CLI, how to convert say BAM to an ADAMs parquet? Same with a canonical 6 columns BED....

Hello, before the ```make duckdb_release release ``` one needs to execute: ``` make ``` DK

**Describe the bug** installation of macs3 inside of the conda environment fails because of "missing" zlib.h and then zconf.h ``` MACS3/fermi-lite/bseq.c:1:10: fatal error: zlib.h: No such file or directory 1...

Hello, in https://github.com/glauth/glauth#quickstart the command from point 4: ``` ldapsearch -LLL -H ldap://localhost:389 -D cn=serviceuser,ou=svcaccts,dc=glauth,dc=com -w mysecret -x -bdc=glauth,dc=com cn=hackers ``` but in sample-simple.cfg ``` [ldap] enabled = true listen...

vt peek enhancement

1

Hello, would it be possible to get the vt peek output in some easier to parse format? Anything like YAML/json will make things easier. Best, Darek Kedra

support for GWAS summary TSV files

1

Hello, The majority of summary stats from various studies & biobanks are available as bgzip-ed TSVs. For converting these to VCF one can use gwas2vcf (https://github.com/MRCIEU/gwas2vcf) but it supports at...

simple example for converting an ofending char to custom string

1

Hello, would it be possible to include, be it in the Readme or some other place a fool proof example how to convert just one bad char to a custom...

Hello, I got a rather strange error message while trying to install RGT package: ``` File "/scratch/dkedra/.conda/envs/rgt_thor/lib/python3.9/site-packages/pkg_resources/__init__.py", line 1420, in get_metadata return value.decode('utf-8') UnicodeDecodeError: 'utf-8' codec can't decode byte 0xa9...

sam-xlate bed format /hg38 / gencode

4

Hello, i have tried: ``` java -jar ./ubu-1.2b-SNAPSHOT-jar-with-dependencies.jar sam-xlate \ --bed gencode.v31.annotation.no_head.bed \ --in test.hg38genome.bam \ --out test.hg38genome.bam ``` I am getting following error: ``` Skipping isoform header order determination...