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updating enclone to changed vdj_ann #406

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9 changes: 4 additions & 5 deletions Cargo.lock
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2 changes: 1 addition & 1 deletion enclone/Cargo.toml
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Expand Up @@ -43,7 +43,7 @@ serde_derive = "1"
serde_json = "1"
stats_utils = "0.1"
string_utils = "0.1"
vdj_ann = "0.4"
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vector_utils = "0.1"

[dev-dependencies]
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40 changes: 36 additions & 4 deletions enclone/src/join.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -432,12 +432,28 @@ pub fn join_exacts(
if !info[k1].has_del[m] {
fwriteln!(log, "chain {}, tig 1", m + 1);
let t1 = DnaString::from_acgt_bytes(tig1);
print_annotations(&t1, refdata, &mut log, false, true, false);
print_annotations(
&t1,
refdata,
&mut log,
false,
true,
false,
Some(ctl.gen_opt.gamma_delta),
);
}
}
if ctl.join_print_opt.ann {
fwriteln!(log, "chain {}, tig 1", m + 1);
print_annotations(&otig1, refdata, &mut log, false, true, false);
print_annotations(
&otig1,
refdata,
&mut log,
false,
true,
false,
Some(ctl.gen_opt.gamma_delta),
);
}
if ctl.join_print_opt.seq {
fwriteln!(log, "\nchain {}, tig 2 = {}", m + 1, otig2.to_string());
Expand All @@ -447,12 +463,28 @@ pub fn join_exacts(
if !info[k2].has_del[m] {
fwriteln!(log, "chain {}, tig 2", m + 1);
let t2 = DnaString::from_acgt_bytes(tig2);
print_annotations(&t2, refdata, &mut log, false, true, false);
print_annotations(
&t2,
refdata,
&mut log,
false,
true,
false,
Some(ctl.gen_opt.gamma_delta),
);
}
}
if ctl.join_print_opt.ann {
fwriteln!(log, "chain {}, tig 2", m + 1);
print_annotations(&otig2, refdata, &mut log, false, true, false);
print_annotations(
&otig2,
refdata,
&mut log,
false,
true,
false,
Some(ctl.gen_opt.gamma_delta),
);
}
}
}
Expand Down
2 changes: 1 addition & 1 deletion enclone_args/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,5 +39,5 @@ regex = { version = "1", default-features = false, features = ["std", "perf"] }
serde_json = "1"
string_utils = "0.1"
tilde-expand = "0.1"
vdj_ann = "0.4"
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vector_utils = "0.1"
10 changes: 9 additions & 1 deletion enclone_args/src/read_json.rs
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Expand Up @@ -203,7 +203,15 @@ fn parse_vector_entry_from_json(
if reannotate || ctl.gen_opt.reprod {
let x = DnaString::from_dna_string(full_seq);
let mut ann = Vec::<(i32, i32, i32, i32, i32)>::new();
annotate_seq(&x, refdata, &mut ann, true, false, true);
annotate_seq(
&x,
refdata,
&mut ann,
true,
false,
true,
Some(ctl.gen_opt.gamma_delta),
);

// If there are multiple V segment alignments, possibly reduce to just one.

Expand Down
2 changes: 1 addition & 1 deletion enclone_com/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -27,5 +27,5 @@ lazy_static = "1"
pretty_trace = "0.5"
string_utils = "0.1"
tokio = { version = "1", default-features = false, features = ["io-util", "macros", "rt-multi-thread"] }
vdj_ann = "0.4"
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}

2 changes: 1 addition & 1 deletion enclone_core/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ stirling_numbers = "0.1"
string_utils = "0.1"
superslice = "1"
tables = "0.1"
vdj_ann = "0.4"
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vector_utils = "0.1"
zstd = "0.9"

Expand Down
4 changes: 2 additions & 2 deletions enclone_denovo/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -39,6 +39,6 @@ stats_utils = "0.1"
string_utils = "0.1"
superslice = "1"
tables = "0.1"
vdj_ann = "0.4"
vdj_ann_ref = { git = "https://github.com/10XGenomics/rust-toolbox.git", rev = "8ed8d7b3186b13c5db6ec7ad3fb8786f111eda65" }
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vdj_ann_ref = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vector_utils = "0.1"
4 changes: 2 additions & 2 deletions enclone_main/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -42,6 +42,6 @@ stats_utils = "0.1"
string_utils = "0.1"
tables = "0.1"
tilde-expand = "0.1"
vdj_ann = "0.4"
vdj_ann_ref = { git = "https://github.com/10XGenomics/rust-toolbox.git", rev = "8ed8d7b3186b13c5db6ec7ad3fb8786f111eda65" }
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vdj_ann_ref = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vector_utils = "0.1"
2 changes: 1 addition & 1 deletion enclone_print/Cargo.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -51,5 +51,5 @@ serde_json = "1"
stats_utils = "0.1"
string_utils = "0.1"
tables = "0.1"
vdj_ann = "0.4"
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vector_utils = "0.1"
2 changes: 1 addition & 1 deletion enclone_proto/Cargo.toml
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Expand Up @@ -25,7 +25,7 @@ prost = { version = "0.9", default_features = false, features = ["std", "prost-d
serde = "1"
serde_derive = "1"
thiserror = "1"
vdj_ann = "0.4"
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}

[build-dependencies]
prost-build = "0.9"
2 changes: 1 addition & 1 deletion enclone_ranger/Cargo.toml
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Expand Up @@ -31,5 +31,5 @@ io_utils = "0.3"
itertools = "0.10"
rayon = "1"
string_utils = "0.1"
vdj_ann = "0.4"
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vector_utils = "0.1"
2 changes: 1 addition & 1 deletion enclone_stuff/Cargo.toml
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Expand Up @@ -38,5 +38,5 @@ regex = { version = "1", default-features = false, features = ["std", "perf"] }
stats_utils = "0.1"
string_utils = "0.1"
tables = "0.1"
vdj_ann = "0.4"
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vector_utils = "0.1"
2 changes: 1 addition & 1 deletion enclone_tail/Cargo.toml
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Expand Up @@ -56,7 +56,7 @@ tables = "0.1"
tar = "0.4"
tiny-skia = "0.6"
usvg = { version = "0.19", features = ["text"] }
vdj_ann = "0.4"
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vector_utils = "0.1"
# to replace by this after bumping version
# vector_utils = "0.1.0"
4 changes: 2 additions & 2 deletions enclone_tools/Cargo.toml
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Expand Up @@ -46,6 +46,6 @@ regex = { version = "1", default-features = false, features = ["std", "perf"] }
serde_json = "1"
stats_utils = "0.1"
string_utils = "0.1"
vdj_ann = "0.4"
vdj_ann_ref = { git = "https://github.com/10XGenomics/rust-toolbox.git", rev = "8ed8d7b3186b13c5db6ec7ad3fb8786f111eda65" }
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vdj_ann_ref = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vector_utils = "0.1"
11 changes: 6 additions & 5 deletions enclone_tools/src/bin/annotate_seq.rs
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Expand Up @@ -98,6 +98,7 @@ fn main() {
gamma_delta = true;
}
}
let is_gd = Some(gamma_delta);

// Make reference data.

Expand Down Expand Up @@ -128,9 +129,9 @@ fn main() {
if ext {
fwriteln!(log, "\nFW ANNOTATION VERSUS PLAIN REFERENCE\n");
}
print_annotations(&seq, &refdata, &mut log, false, true, verbose);
print_annotations(&seq, &refdata, &mut log, false, true, verbose, is_gd);
let mut ann = Vec::<(i32, i32, i32, i32, i32)>::new();
annotate_seq(&seq, &refdata, &mut ann, true, false, true);
annotate_seq(&seq, &refdata, &mut ann, true, false, true, is_gd);
print_cdr3_using_ann(&seq, &refdata, &ann, &mut log);
print_start_codon_positions(&seq, &mut log);
if is_valid(&seq, &refdata, &ann, true, &mut log, Some(gamma_delta)) {
Expand Down Expand Up @@ -255,16 +256,16 @@ fn main() {
if ext {
let seq_rc = seq.rc();
fwriteln!(log, "\nRC ANNOTATION VERSUS PLAIN REFERENCE\n");
print_annotations(&seq_rc, &refdata, &mut log, false, false, verbose);
print_annotations(&seq_rc, &refdata, &mut log, false, false, verbose, is_gd);

// Annotate using the extended reference.

let mut refdatax = RefData::new();
make_vdj_ref_data(&mut refdatax, imgt, &species, true, is_tcr, is_bcr);
fwriteln!(log, "\nFW ANNOTATION VERSUS EXTENDED REFERENCE\n");
print_annotations(&seq, &refdatax, &mut log, false, false, verbose);
print_annotations(&seq, &refdatax, &mut log, false, false, verbose, is_gd);
fwriteln!(log, "\nRC ANNOTATION VERSUS EXTENDED REFERENCE\n");
print_annotations(&seq_rc, &refdatax, &mut log, false, false, verbose);
print_annotations(&seq_rc, &refdatax, &mut log, false, false, verbose, is_gd);
}

// Print.
Expand Down
4 changes: 2 additions & 2 deletions master.toml
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Expand Up @@ -103,7 +103,7 @@ tonic = { version = "0.6", default-features = false, features = ["transport", "c
tonic-build = { version = "0.6", default-features = false, features = ["transport", "prost"] }
users = "0.11"
usvg = { version = "0.19", features = ["text"] }
vdj_ann = "0.4"
vdj_ann_ref = { git = "https://github.com/10XGenomics/rust-toolbox.git", rev = "8ed8d7b3186b13c5db6ec7ad3fb8786f111eda65" }
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vdj_ann = { git = "https://github.com/10XGenomics/rust-toolbox.git", branch = "nmmsv/missing-gd-features"}
vector_utils = "0.1"
yaml-rust = "0.4"