Closed mbhall88 closed 2 months ago
= note: expected struct `noodles_cram::Record` found reference `&dyn noodles_sam::alignment::Record`
Is that a change that should be made in a separate PR?
For now, convert &dyn sam::alignment::Record
to a cram::Record
using cram::Record::try_from_alignment_record
. I can normalize the interfaces after this patch.
In addition, I also noticed some slight differences in function naming schemes between SAM/BAM and CRAM. For example, the SAM and BAM async
Writer
s have awrite_header
function, however, the reciprocal CRAM function iswrite_file_header
- not sure if this was intended though.
Yes, this is intentional. I/O is modeled after the physical structure for the format (see § 5 "File structure" (2024-03-21) for a visual representation). The file header is named to differentiate itself from the many other headers in the format, e.g., the container header, the slice header, the block header, etc. I did add a convenience method to the blocking reader in 2da4eae513c3de8b7ecd64ff0246fa61c56a58bb, which simply needs to be synchronized with the async reader later. Use the currently available methods to write a default file definition, and use the SAM header to write the file header, e.g.,
Also, the CRAM async builder has the function
build_with_writer
rather than thebuild_from_writer
.
Good catch; it's definitely a typo. Use the methods that are currently available. I can also fix this after this patch.
Further to the above, when adding the async Writer example I realised I had missed adding Writer::finish
. Again, the individual BAM and CRAM methods that are analogous are called shutdown
instead of finish
. I took the name finish to mirror the sync alignment API. Not sure if these too should be harmonised?
Aside from that, I think this PR is done and ready for review.
See #286 for more details.
Checklist
examples/
entryCurrently, I cannot compile the async Writer due to
Which is coming from the fact that
cram::async::io::Writer::write_record
takes acram::Record
type rather than a&dyn sam::alignment::Record
trait.https://github.com/zaeleus/noodles/blob/174ad3c98092728a6be3feabb346619ebd14a5ad/noodles-cram/src/async/io/writer.rs#L184
Is that a change that should be made in a separate PR?
In addition, I also noticed some slight differences in function naming schemes between SAM/BAM and CRAM. For example, the SAM and BAM async
Writer
s have awrite_header
function, however, the reciprocal CRAM function iswrite_file_header
- not sure if this was intended though. Also, the CRAM async builder has the functionbuild_with_writer
rather than thebuild_from_writer
. I appreciate these are minor things, but thought I would raise them in case you want to move this library towards consistent names across modules/crates. I guess for backwards compatibility we could add the [#[deprecated
](https://doc.rust-lang.org/reference/attributes/diagnostics.html#the-deprecated-attribute) attribute if you want to introduce the consistent named version.