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feat: Return the status of unproductive contigs in is_valid function #287

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feat: Return the status of unproductive contigs in is_valid function #287

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d7aa187
added a prelim test
nmmsv10x Aug 23, 2023
ca66019
added telemetry for unproductive reasoning
nmmsv10x Aug 23, 2023
86c8f20
added tooLarge
nmmsv10x Aug 23, 2023
b5b1c01
added prints
nmmsv10x Aug 23, 2023
cadb726
updated telem
nmmsv10x Aug 23, 2023
6ab352a
updated telem
nmmsv10x Aug 23, 2023
ceb0c14
update
nmmsv10x Aug 23, 2023
42d6f93
update
nmmsv10x Aug 23, 2023
780cb67
added all failing tests
nmmsv10x Aug 23, 2023
a6193cc
update telem
nmmsv10x Aug 23, 2023
91cabdd
using a smaller ref for tests
nmmsv10x Aug 24, 2023
762c378
added a productive case to the test
nmmsv10x Aug 24, 2023
6b1857b
added test data to repo
nmmsv10x Aug 24, 2023
067eb0f
remove comment
nmmsv10x Aug 24, 2023
11424d9
use object return instead of tuple
nmmsv10x Aug 24, 2023
7ea1499
don't jump out when no cdr3
nmmsv10x Aug 24, 2023
78da3a3
remove extra return
nmmsv10x Aug 24, 2023
d7f06d4
fix clippy error
nmmsv10x Aug 24, 2023
914ae09
parsing ann into a rust object for better readability
nmmsv10x Aug 30, 2023
dbd054d
use bitflags for unproductive cause
nmmsv10x Aug 30, 2023
6b9c957
added new error modes
nmmsv10x Aug 30, 2023
d35f98c
remove >>s
nmmsv10x Aug 30, 2023
16a96cf
loosen't productivity
nmmsv10x Aug 30, 2023
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1 change: 1 addition & 0 deletions Cargo.lock
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1 change: 1 addition & 0 deletions vdj_ann/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -26,3 +26,4 @@ stats_utils = { version = "0.1", path = "../stats_utils" }
string_utils = { version = "0.1", path = "../string_utils" }
vector_utils = { version = "0.1", path = "../vector_utils" }
vdj_types = { version = "0.2", path = "../vdj_types" }
bitflags = "2.4.0"
18 changes: 7 additions & 11 deletions vdj_ann/src/annotate.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -8,21 +8,17 @@
use align_tools::affine_align;
use amino::{aa_seq, have_start};
use bio_edit::alignment::AlignmentOperation::{Del, Ins, Match, Subst, Xclip, Yclip};
use debruijn::{
dna_string::{DnaString, DnaStringSlice},
kmer::{Kmer12, Kmer20},
Mer, Vmer,
};
use debruijn::dna_string::{DnaString, DnaStringSlice};
use debruijn::kmer::{Kmer12, Kmer20};
use debruijn::{Mer, Vmer};
use io_utils::{fwrite, fwriteln};
use itertools::Itertools;
use serde::{Deserialize, Serialize};
use stats_utils::percent_ratio;
use std::cmp::{max, min};
use std::fmt::Write as _;
use std::{
cmp::{max, min},
fs::File,
io::{BufWriter, Write},
};
use std::fs::File;
use std::io::{BufWriter, Write};
use string_utils::{stringme, strme, TextUtils};
use vdj_types::{VdjChain, VdjRegion};
use vector_utils::{
Expand Down Expand Up @@ -228,16 +224,16 @@
}
}

pub fn annotate_seq_core(
b: &DnaString,
refdata: &RefData,
ann: &mut Vec<(i32, i32, i32, i32, i32)>,
allow_weak: bool,
allow_improper: bool,
abut: bool,
log: &mut Vec<u8>,
verbose: bool,
) {

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this function has too many arguments (8/7) 

warning: this function has too many arguments (8/7)
   --> vdj_ann/src/annotate.rs:227:1
    |
227 | / pub fn annotate_seq_core(
228 | |     b: &DnaString,
229 | |     refdata: &RefData,
230 | |     ann: &mut Vec<(i32, i32, i32, i32, i32)>,
...   |
235 | |     verbose: bool,
236 | | ) {
    | |__^
    |
    = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#too_many_arguments
    = note: `#[warn(clippy::too_many_arguments)]` on by default
// The DNA string representation is inefficient because it stores bases as packed k-mers
// which requires a lot of array bounds checks when unpacking which was a hot path
// we found when profiling the CI job. To avoid those in the inner
Expand Down Expand Up @@ -1596,8 +1592,8 @@
// deletion. Be very careful to respect this if editing!

let (mut win1, mut win2) = (false, false);
let c1 = m1 == m2 && !have_utr_align2 && err1_nu == err2_nu && outside1 > outside2;

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strict comparison of `f32` or `f64` 

warning: strict comparison of `f32` or `f64`
    --> vdj_ann/src/annotate.rs:1595:54
     |
1595 |             let c1 = m1 == m2 && !have_utr_align2 && err1_nu == err2_nu && outside1 > outside2;
     |                                                      ^^^^^^^^^^^^^^^^^^ help: consider comparing them within some margin of error: `(err1_nu - err2_nu).abs() < error_margin`
     |
     = note: `f32::EPSILON` and `f64::EPSILON` are available for the `error_margin`
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#float_cmp
     = note: requested on the command line with `-W clippy::float-cmp`
let c2 = m2 == m1 && !have_utr_align1 && err2_nu == err1_nu && outside2 > outside1;

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strict comparison of `f32` or `f64` 

warning: strict comparison of `f32` or `f64`
    --> vdj_ann/src/annotate.rs:1596:54
     |
1596 |             let c2 = m2 == m1 && !have_utr_align1 && err2_nu == err1_nu && outside2 > outside1;
     |                                                      ^^^^^^^^^^^^^^^^^^ help: consider comparing them within some margin of error: `(err2_nu - err1_nu).abs() < error_margin`
     |
     = note: `f32::EPSILON` and `f64::EPSILON` are available for the `error_margin`
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#float_cmp
if (zstop1 > zstop2 + 20 && (outside2 <= 10.0 || total2 - share <= 10))
|| (outside1 >= 10.0 && outside2 <= 1.0 && err1 - err2 <= 2.5)
{
Expand All @@ -1606,8 +1602,8 @@
} else if (outside2 <= 10.0 || total2 - share <= 10)
&& (m1 < m2
|| (m1 == m2 && err1 < err2 && !c2)
|| (m1 == m2 && err1 == err2 && outside1 > outside2)

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strict comparison of `f32` or `f64` 

warning: strict comparison of `f32` or `f64`
    --> vdj_ann/src/annotate.rs:1605:37
     |
1605 |                     || (m1 == m2 && err1 == err2 && outside1 > outside2)
     |                                     ^^^^^^^^^^^^ help: consider comparing them within some margin of error: `(err1 - err2).abs() < error_margin`
     |
     = note: `f32::EPSILON` and `f64::EPSILON` are available for the `error_margin`
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#float_cmp
|| (m1 == m2 && err1 == err2 && outside1 == outside2 && t1 < t2)

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strict comparison of `f32` or `f64` 

warning: strict comparison of `f32` or `f64`
    --> vdj_ann/src/annotate.rs:1606:37
     |
1606 |                     || (m1 == m2 && err1 == err2 && outside1 == outside2 && t1 < t2)
     |                                     ^^^^^^^^^^^^ help: consider comparing them within some margin of error: `(err1 - err2).abs() < error_margin`
     |
     = note: `f32::EPSILON` and `f64::EPSILON` are available for the `error_margin`
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#float_cmp

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strict comparison of `f32` or `f64` 

warning: strict comparison of `f32` or `f64`
    --> vdj_ann/src/annotate.rs:1606:53
     |
1606 |                     || (m1 == m2 && err1 == err2 && outside1 == outside2 && t1 < t2)
     |                                                     ^^^^^^^^^^^^^^^^^^^^ help: consider comparing them within some margin of error: `(outside1 - outside2).abs() < error_margin`
     |
     = note: `f32::EPSILON` and `f64::EPSILON` are available for the `error_margin`
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#float_cmp
|| c1)
{
win1 = true;
Expand All @@ -1623,8 +1619,8 @@
} else if (outside1 <= 10.0 || total1 - share <= 10)
&& (m2 < m1
|| (m2 == m1 && err2 < err1 && !c1)
|| (m2 == m1 && err2 == err1 && outside2 > outside1)

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strict comparison of `f32` or `f64` 

warning: strict comparison of `f32` or `f64`
    --> vdj_ann/src/annotate.rs:1622:37
     |
1622 |                     || (m2 == m1 && err2 == err1 && outside2 > outside1)
     |                                     ^^^^^^^^^^^^ help: consider comparing them within some margin of error: `(err2 - err1).abs() < error_margin`
     |
     = note: `f32::EPSILON` and `f64::EPSILON` are available for the `error_margin`
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#float_cmp
|| (m2 == m1 && err2 == err1 && outside2 == outside1 && t2 < t1)

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strict comparison of `f32` or `f64` 

warning: strict comparison of `f32` or `f64`
    --> vdj_ann/src/annotate.rs:1623:37
     |
1623 |                     || (m2 == m1 && err2 == err1 && outside2 == outside1 && t2 < t1)
     |                                     ^^^^^^^^^^^^ help: consider comparing them within some margin of error: `(err2 - err1).abs() < error_margin`
     |
     = note: `f32::EPSILON` and `f64::EPSILON` are available for the `error_margin`
     = help: for further information visit https://rust-lang.github.io/rust-clippy/master/index.html#float_cmp
|| c2)
{
win2 = true;
Expand Down Expand Up @@ -3179,7 +3175,7 @@
let mut ann = Vec::<(i32, i32, i32, i32, i32)>::new();
annotate_seq(b, refdata, &mut ann, true, false, true);
let mut log = Vec::<u8>::new();
let productive = is_valid(b, refdata, &ann, false, &mut log, is_gd);
let productive = is_valid(b, refdata, &ann, false, &mut log, is_gd).productive;
ContigAnnotation::from_annotate_seq(
b,
q,
Expand Down
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