Bug when calling --dump_sample_anchor_target_count_binary

[miramou]

Hi! Thanks so much for this package.

I downloaded your pre-compiled code and tested using the example. Running 'run-example.sh' works as expected.

When I run the following: ../splash --bin_path .. --dump_sample_anchor_target_count_binary input.txt

The code fails at stage 2 and points to stage 2's log files. The key line in the log is: Error: cannot open file PATH_TO_EXAMPLE/example/test_satc/bin13.satc

This is resolved if I create the directory test_satc with mkdir before re-running the command. But I'd expect the code to create the output directory for me as written so it looks like a bug. It'd be helpful if this were resolved in future releases though the workaround at the moment is easy.

One other thing I noticed is that when I specify an absolute path as follows using 'outname_prefix' the code fails as well: ../splash --bin_path .. --dump_sample_anchor_target_count_binary --outname_prefix "PATH_TO_EXAMPLE/test" input.txt Error: cannot open file splash-tmp-3c5d50e0104b4269a11bd42bf88f6ebd/PATH_TO_EXAMPLE/test.bin11.stats.tsv This seems like less of an issue but it'd be helpful to note that outname_prefix is only relative.

Best, Mira

[marekkokot]

Hi! Thank you for reporting this and using splash. We have an unpublished version of the code. I just checked and the first issue you described is solved in the new version, so this will be available when we integrate our unpublished code with this repository (hard to say when we work intensively).

The second part is more problematic since it also crashes on newer version of the code. I will try to address this, for a quick inspection I think there should be no need to require a relative path, so I will try to fix this.

Thanks again for pointing these issues :)

[miramou]

Great thanks!