problem opening file: -B in preseq with ./configure --enable-hts option

[h20gg702]

Dear developers,
PEPATAC_log2.md
PEPATAC_log1.md

Thanks for developing wonderful package. I got a problem when I try to do extended tutorial like below. When I installed preseq, I used ./configure --enable-hts option to read in bam input. Do you have any solution for this?

preseq c_curve -v -o /home1/yoshiaki/pepatac_tutorial/processed/results_pipeline/tutorial2/QC_hg38/tutorial2_preseq_out.txt -B /home1/yoshiaki/pepatac_tutorial/processed/results_pipeline/tutorial2/aligned_hg38/tutorial2_sort.bam (219566)

<pre>
BED_INPUT
ERROR:	problem opening file: -B`

Thanks in advance.

[nsheff]

What version of preseq are you using?

preseq --version
unrecognized command: --version
preseq:  a program for analyzing library complexity
Version: 2.0.3

When I run that command, it works correctly.

[nsheff]

@donaldcampbelljr we might want to update PEPATAC to use the latest preseq; there is a v3.x series available now.

To do this, we would need to:

• Figure out if the API changed in the new preseq. It looks like it might expect the -B to come before the -o now.
• Release a new bulker crate with the upgraded preseq. that would be quay.io/biocontainers/preseq:3.2.0--hdcf5f25_6 (see: https://quay.io/repository/biocontainers/preseq?tab=tags)
• Update the pepatac code when it constructs the commands to make sure they do it right.
• Make sure the output is compatible with what we do downstream with it.
• Update documentation to reflect the new preseq version requirement, and bulker create number
• Release updated pepatac version.

[nsheff]

@h20gg702 in the short term, you can try installing a v2.x series of preseq and I think it should work.

[donaldcampbelljr]

Related to: smithlabcode/preseq#74