plot-vcfstats -s leads to IndexError: list index out of range

[warthmann]

Hello,

bcftools view input.vcf.gz | bcftools stats -s - > file.vchk
plot-vcfstats -p outdir file.vchk

works perfectly, but when I want sample names instead of indices, ie use the -s flag, it throws an index error

(ngs-tools) norman@norman-Workstation:$ plot-vcfstats -s -p outdir file.vchk
Parsing bcftools stats output: file.vchk
Plotting graphs: python3 plot.py
Traceback (most recent call last):
  File "/mnt/data/norman/Analysis/banana/TR4_SEQ2020/Analysis-Aug2024/Results-SNP-Analysis/outdir/plot.py", line 601, in <module>
    plt.xticks([int(row[0]) for row in dat],[row[7] for row in dat],**sample_font)
                                             ~~~^^^
IndexError: list index out of range
The command exited with non-zero status 256:
	python3 plot.py

 at xxx/miniconda3/envs/ngs-tools/bin/plot-vcfstats line 116.
	main::error("The command exited with non-zero status 256:\x{a}\x{9}python3 plot.py\x{a}\x{a}") called at xxx/miniconda3/envs/ngs-tools/bin/plot-vcfstats line 311
	main::plot(HASH(0x56199d6bbed0)) called at xxx/miniconda3/envs/ngs-tools/bin/plot-vcfstats line 75

any help is greatly appreciated. My vcf file contains 5 samples, and it occurs whether or not I list them in the bcftools stats -s commandline.

I am on Ubuntu 20 in a conda environment with
bcftools 1.21
matplotlib 3.10.0
Python 3.13.1

thanks a lot!

[pd3]

I was unable to reproduce the problem. Can you share the stats output, file.vchk?

[warthmann]

Sure, thank you for your time. I had to add suffix .txt. or github would not let me upload.
S-diploid~filtered-default.vchk.txt

[nbesteban]

Hi,

I get the same Index error when using sample names in the vcf plot stats.
Looking forward to the solution as well. :)

[pd3]

@nbesteban Can you open a new issue and attach a test file please?

[nbesteban]

@pd3 I adopted your recent commit. Now it works! Thank you!