Torsten Seemann

I asked for the help, and got it. It's not an error. (i'm packaging for brew)

samtools view -bSu in pipe is now redundant

1

FYI, the samtools view is not needed since version 1.3 (or earlier possibly) ``` java -jar build/libs/bazam.jar -bam my.bam | \ bwa mem -p ref.fa - | \ samtools view...

FYI - https://github.com/Homebrew/homebrew-science/pull/2468

Official abbreviations for antibiotics/drugs

4

[EUCAST_system_for_antimicrobial_abbreviations.pdf](https://github.com/arpcard/amr_curation/files/3765111/EUCAST_system_for_antimicrobial_abbreviations.pdf) Should we consider adding or using the 3 letter EUCAST codes for drug names to the ARO ?

Major behaviour change from 1.0.7 to 1.1.1

4

Today I upgraded from lighter 1.0.7 to 1.1.1 and I first noticed a problem when 1.1.1 was outputting different number of reads in the two output files, and then noticed...

In function `print_usage': nw_cmdline.c undefined reference to `string_buff_strlen'

5

This is `bash install.sh` result now: ``` for file in ; do rm -r $file; done for file in ; do rm $file; done gcc -o needleman_wunsch -O3 -DCOMPILE_TIME='"Thu Mar...

I assume the beginning of krocus is building some index? i get no messages about it

Inconsistent predictions of G from ground truth set

2

Pall, I have a bacterial genome 2866389 bp (2.8 Mbp) which is finished/closed and a set of Illumina PE reads to 90x coverage. I ran the following for Q =...

ValueError: f(a) and f(b) must have different signs

1

Error on a 1K amplicon: ``` cat raw.tsv Q k F0 f1 F1 0 21 964 0 271790 0 27 952 0 247142 0 33 954 0 222535 0 39...

The python script fails if i use some k-mers longer than the read length: ``` Q k F0 f1 F1 0 121 0 0 0 Division by zero error. ```