Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix: bam::Record:new should return a valid record #361

Merged
merged 13 commits into from
May 22, 2024
Merged

fix: bam::Record:new should return a valid record #361

Changes from 2 commits
Commits
Show all changes
13 commits
Select commit Hold shift + click to select a range
4db8850
bam::Record:new should return a valid record
nh13 Jun 17, 2022
a3278b9
Update record.rs
nh13 Jun 18, 2022
cf5bf1a
Update src/bam/record.rs
nh13 Jun 18, 2022
cacc1f3
Update mod.rs
nh13 Jun 18, 2022
f02c86e
fix whitespaces
nh13 Jun 18, 2022
7e3fd68
Update mod.rs
nh13 Jun 18, 2022
5ddbd6b
Update mod.rs
nh13 Jun 19, 2022
1aaad6f
Update src/bam/mod.rs
nh13 Jun 19, 2022
2b47d10
Update src/bam/mod.rs
nh13 Jun 29, 2022
81013f9
fix
nh13 Jun 30, 2022
9cd847d
fix
nh13 Jun 30, 2022
4a51951
Merge branch 'master' into patch-3
brainstorm May 19, 2024
d4bc492
review fixup
nh13 May 22, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
11 changes: 9 additions & 2 deletions src/bam/record.rs
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -113,12 +113,19 @@ fn extranul_from_qname(qname: &[u8]) -> usize {
impl Record {
/// Create an empty BAM record.
pub fn new() -> Self {
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The goal in this PR is to that one does not need to call any other methods on Record to have a valid record. Currently, this requires setting the read name and alignment positions (and unmapped flag if the positions are -1). So this PR has an opinion, that a new record is unmapped with empty name/seq/qual/cigar.

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Thanks for indirectly making me think about Default trait vs new(): https://users.rust-lang.org/t/when-to-use-default-trait/11190

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Coincidental good read on Default: https://cj.rs/blog/rust-default-values-for-maintainability/

Record {
let record = Record {
nh13 marked this conversation as resolved.
Show resolved Hide resolved
inner: unsafe { MaybeUninit::zeroed().assume_init() },
own: true,
cigar: None,
header: None,
}
};
// Developer note: these are needed so the returned record is properly
// initialized as unmapped.
record.set_tid(-1);
record.set_pos(-1);
record.set_mpos(-1);
record.set_mtid(-1);
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I would argue that we should also set the record to be unmapped by default. I mean, how can it be mapped if the tid/pos are -1?

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Sounds reasonable but I'd quickly compare third party implementations (htslib/htsjdk/noodles) and/or spec footnotes (lots of gotchas there).

record
}

pub fn from_inner(from: *mut htslib::bam1_t) -> Self {
Expand Down