Extract reads from BAM in version 0.3.0 / Could not read the header of the input file

[pkerbs]

Hi @mbhall88,
thank you for your work on that. I finally found some time to test it and unfortunately, I encountered an issue with this new version.
I just run the new version on a BAM file like this:

ontime test.bam --to 2h > test_2h.bam

and got this error message:

[2024-02-12T20:25:09Z INFO ] Extracting read start times...
[2024-02-12T20:25:14Z INFO ] Gathered start times for 146140 reads
[2024-02-12T20:25:14Z INFO ] First and last timestamps in the input are 2024-02-08T15:24:22.872Z and 2024-02-09T16:35:34.702Z
[2024-02-12T20:25:14Z INFO ] Extracting reads with a start time between 2024-02-08 15:24:22.872 and 2024-02-08 17:24:22.872...
Error: Could not read the header of the input file

Caused by:
    invalid BAM header

The BAM file was generated by Dorado v0.5.2 like this:

dorado basecaller \
  sup,5mCG_5hmCG \
  <path to pod5 files> \
  --reference ref/chm13v2.fa \
  --bandwidth 500,20000 \
  -Y

Did I execute it wrong somehow, or missed a parameter for the header?
Thanks in advance.
Kind regards,
Paul

Originally posted by @pkerbs in #6 (comment)

[mbhall88]

Thanks for picking this up. No idea how I didn't see this in testing. v0.3.1 has the fix

[pkerbs]

Thank you so much, works like a charm.
Waiting for the release on Bioconda :)

[mbhall88]

Waiting for the release on Bioconda :)

Just merged, so shouldn't be too long