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refactor: Extract repeated H5 loading code into a couple of small types #548

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merged 4 commits into from
Apr 2, 2024
Merged

refactor: Extract repeated H5 loading code into a couple of small types #548

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9797882
Finish extracting/simplifying H5 loading.
macklin-10x Mar 26, 2024
c65a2a9
Point back to feature branch.
macklin-10x Mar 26, 2024
64f171e
update enclone_ranger
macklin-10x Apr 2, 2024
f513c77
Point back to main.
macklin-10x Apr 2, 2024
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59 changes: 30 additions & 29 deletions Cargo.lock
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33 changes: 3 additions & 30 deletions enclone_main/src/stop.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -35,32 +35,7 @@ pub fn main_enclone_stop(
let ctl = &setup.ctl;
let tall = &setup.tall.unwrap();

// Load the GEX and FB data. This is quite horrible: the code and computation are duplicated
// verbatim in fcell.rs.

let mut d_readers = Vec::<Option<Reader>>::new();
let mut ind_readers = Vec::<Option<Reader>>::new();
for li in 0..ctl.origin_info.n() {
if !ctl.origin_info.gex_path[li].is_empty() {
let x = gex_info.h5_data[li].as_ref();
d_readers.push(Some(x.unwrap().as_reader()));
ind_readers.push(Some(gex_info.h5_indices[li].as_ref().unwrap().as_reader()));
} else {
d_readers.push(None);
ind_readers.push(None);
}
}
let mut h5_data = Vec::<(usize, Vec<u32>, Vec<u32>)>::new();
for li in 0..ctl.origin_info.n() {
h5_data.push((li, Vec::new(), Vec::new()));
}
h5_data.par_iter_mut().for_each(|res| {
let li = res.0;
if !ctl.origin_info.gex_path[li].is_empty() && ctl.gen_opt.h5_pre {
res.1 = d_readers[li].as_ref().unwrap().read_raw().unwrap();
res.2 = ind_readers[li].as_ref().unwrap().read_raw().unwrap();
}
});
let gex_readers = setup.create_gex_readers();

// Find and print clonotypes. (But we don't actually print them here.)
if !ctl.gen_opt.trace_barcode.is_empty() {
Expand All @@ -85,7 +60,7 @@ pub fn main_enclone_stop(
mut rsi,
mut out_datas,
gene_scan_result,
} = print_clonotypes(setup, exacts, &d_readers, &ind_readers, &h5_data, &fate)?;
} = print_clonotypes(setup, exacts, &gex_readers, &fate)?;

// Gather some data for gene scan.
let (mut tests, mut controls) = (vec![], vec![]);
Expand Down Expand Up @@ -197,9 +172,7 @@ pub fn main_enclone_stop(
&fate,
&tests,
&controls,
&h5_data,
&d_readers,
&ind_readers,
&gex_readers,
drefs,
&groups,
&opt_d_val,
Expand Down
47 changes: 9 additions & 38 deletions enclone_tail/src/tail.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ use crate::group::group_and_print_clonotypes;

use enclone_core::defs::{ColInfo, EncloneControl, ExactClonotype, GexInfo};

use enclone_core::enclone_structs::{BarcodeFates, JoinInfo};
use enclone_core::enclone_structs::{BarcodeFates, GexReaders, JoinInfo};
use enclone_proto::types::DonorReferenceItem;
use io_utils::fwrite;
use ndarray::s;
Expand Down Expand Up @@ -39,9 +39,7 @@ pub fn tail_code(
fate: &[BarcodeFates],
tests: &Vec<usize>,
controls: &Vec<usize>,
h5_data: &Vec<(usize, Vec<u32>, Vec<u32>)>,
d_readers: &Vec<Option<Reader>>,
ind_readers: &Vec<Option<Reader>>,
gex_readers: &[Option<GexReaders<'_>>],
dref: &Vec<DonorReferenceItem>,
groups: &Vec<Vec<(i32, String)>>,
opt_d_val: &Vec<(usize, Vec<Vec<Vec<usize>>>)>,
Expand Down Expand Up @@ -175,23 +173,11 @@ pub fn tail_code(
let z2 = gex_info.h5_indptr[li][p as usize + 1] as usize;
let d: Vec<u32>;
let ind: Vec<u32>;
if ctl.gen_opt.h5_pre {
d = h5_data[li].1[z1..z2].to_vec();
ind = h5_data[li].2[z1..z2].to_vec();
} else {
d = d_readers[li]
.as_ref()
.unwrap()
.read_slice(s![z1..z2])
.unwrap()
.to_vec();
ind = ind_readers[li]
.as_ref()
.unwrap()
.read_slice(s![z1..z2])
.unwrap()
.to_vec();
}
let (d, ind) = gex_readers[li]
.as_ref()
.unwrap()
.get_range(z1..z2)
.unwrap();
for j in 0..d.len() {
if ind[j] == fid as u32 {
raw_count = d[j] as f64;
Expand Down Expand Up @@ -228,23 +214,8 @@ pub fn tail_code(
let z2 = gex_info.h5_indptr[li][p as usize + 1] as usize;
let d: Vec<u32>;
let ind: Vec<u32>;
if ctl.gen_opt.h5_pre {
d = h5_data[li].1[z1..z2].to_vec();
ind = h5_data[li].2[z1..z2].to_vec();
} else {
d = d_readers[li]
.as_ref()
.unwrap()
.read_slice(s![z1..z2])
.unwrap()
.to_vec();
ind = ind_readers[li]
.as_ref()
.unwrap()
.read_slice(s![z1..z2])
.unwrap()
.to_vec();
}
let (d, ind) =
gex_readers[li].as_ref().unwrap().get_range(z1..z2).unwrap();
for j in 0..d.len() {
if ind[j] == fid as u32 {
raw_count = d[j] as f64;
Expand Down