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Refactor bigtools internals and API for writing #45

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merged 31 commits into from
Jul 5, 2024
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452f0d7
WIP Refactor ChromData
jackh726 Apr 18, 2024
fd8ba7f
WIP convert StreamingIterator to new ChromData
jackh726 Apr 19, 2024
85acb06
Create ChromProcess trait
jackh726 Apr 19, 2024
3d7a802
Pass trait to new ChromData
jackh726 Apr 19, 2024
e4126d8
Return instance of trait
jackh726 Apr 19, 2024
ba99b5b
Inline process_chrom fns and move beginnings to create fn
jackh726 Apr 19, 2024
392404e
Pass back P and destroy to get data
jackh726 Apr 19, 2024
4d527c2
It works
jackh726 Apr 19, 2024
cb2c5cd
Problems
jackh726 Apr 20, 2024
4c21582
Don't call block_on inside task
jackh726 Apr 20, 2024
4523905
Use FileView for BedParserParallelStreamingIterator
jackh726 Apr 20, 2024
c647ee0
Uplift Value and Error from ChromValues to ChromData
jackh726 Apr 20, 2024
cf0dc85
Remove ChromValues
jackh726 Apr 20, 2024
28c2425
Remove BedParser and fold logic instead in process_to_bbi. Also fix c…
jackh726 Apr 21, 2024
3f3e9bd
A couple minor things
jackh726 Apr 21, 2024
03bd96c
Make do_read in write_vals a fn
jackh726 Apr 21, 2024
583cbcb
Don't box for ChromProcessingInputSectionChannel
jackh726 Apr 21, 2024
c8fb881
Stop using remote_handle
jackh726 Apr 21, 2024
6300bcd
Minor cleanups
jackh726 Apr 21, 2024
f9bc25a
Fix perf for BedParserStreamingIterator by moving out block_on and re…
jackh726 May 7, 2024
d186edb
Add Send bound to Er
jackh726 May 7, 2024
41dffe9
Mostly fix parallelism in bigwigtobedgraph and bigbedtobed
jackh726 May 8, 2024
e018c4a
Cleanup bedchromdata function
jackh726 Jun 26, 2024
041d652
Eagerly check error
jackh726 Jun 26, 2024
ad8937a
Use &mut instead of passing by val to eliminate memmoves
jackh726 Jun 26, 2024
de00dab
Bump to 0.5.0-dev
jackh726 Jun 28, 2024
29cef5f
Rename ChromData to BBIDataSource and ChromProcess to BBIDataProcesso…
jackh726 Jul 4, 2024
6266931
Rename ProcessChromError to BBIProcessError and make do_process retur…
jackh726 Jul 4, 2024
d8b1878
Use ProcessDataError instead of BBIProcessError basically everywhere
jackh726 Jul 4, 2024
6083808
One pub -> pub(crate)
jackh726 Jul 4, 2024
e446a6e
Make create_file and open_file take . Abstract BigWigWrite and BigBed…
jackh726 Jul 5, 2024
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2 changes: 1 addition & 1 deletion Cargo.lock

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2 changes: 1 addition & 1 deletion bigtools/Cargo.toml
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
[package]
name = "bigtools"
version = "0.4.4-dev"
version = "0.5.0-dev"
authors = ["Jack Huey <jackh726@gmail.com>"]
edition = "2021"
license = "MIT"
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2 changes: 1 addition & 1 deletion bigtools/src/bbi.rs
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ pub(crate) mod bbiread;
#[cfg(feature = "write")]
pub(crate) mod bbiwrite;
#[cfg(feature = "write")]
pub mod bedchromdata;
pub mod beddata;
#[cfg(feature = "read")]
pub(crate) mod bigbedread;
#[cfg(feature = "write")]
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4 changes: 2 additions & 2 deletions bigtools/src/bbi/bbiread.rs
Original file line number Diff line number Diff line change
Expand Up @@ -501,8 +501,8 @@ impl GenericBBIRead<ReopenableFile> {
/// Opens a generic bbi file
pub fn open_file(path: &str) -> Result<Self, GenericBBIFileOpenError> {
let reopen = ReopenableFile {
path: path.to_string(),
file: File::open(path)?,
file: File::open(&path)?,
path: path.into(),
};
let b = GenericBBIRead::open(reopen);
if b.is_err() {
Expand Down
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