up

Cargo.lock

@@ -99,6 +99,21 @@ dependencies = [
  "num-traits",
 ]
 
+[[package]]
+name = "arrayvec"
+version = "0.7.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "96d30a06541fbafbc7f82ed10c06164cfbd2c401138f6addd8404629c4b16711"
+
+[[package]]
+name = "atomic-polyfill"
+version = "1.0.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8cf2bce30dfe09ef0bfaef228b9d414faaf7e563035494d7fe092dba54b300f4"
+dependencies = [
+ "critical-section",
+]
+
 [[package]]
 name = "autocfg"
 version = "1.3.0"
@@ -297,6 +312,12 @@ dependencies = [
  "cc",
 ]
 
+[[package]]
+name = "cobs"
+version = "0.2.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "67ba02a97a2bd10f4b59b25c7973101c79642302776489e030cd13cdab09ed15"
+
 [[package]]
 name = "colorchoice"
 version = "1.0.2"
@@ -337,6 +358,12 @@ dependencies = [
  "cfg-if",
 ]
 
+[[package]]
+name = "critical-section"
+version = "1.1.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7059fff8937831a9ae6f0fe4d658ffabf58f2ca96aa9dec1c889f936f705f216"
+
 [[package]]
 name = "crossbeam-channel"
 version = "0.5.13"
@@ -514,6 +541,12 @@ version = "1.13.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "60b1af1c220855b6ceac025d3f6ecdd2b7c4894bfe9cd9bda4fbb4bc7c0d4cf0"
 
+[[package]]
+name = "embedded-io"
+version = "0.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ef1a6892d9eef45c8fa6b9e0086428a2cca8491aca8f787c534a3d6d0bcb3ced"
+
 [[package]]
 name = "encode_unicode"
 version = "0.3.6"
@@ -628,6 +661,15 @@ dependencies = [
  "crunchy",
 ]
 
+[[package]]
+name = "hash32"
+version = "0.2.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b0c35f58762feb77d74ebe43bdbc3210f09be9fe6742234d573bacc26ed92b67"
+dependencies = [
+ "byteorder",
+]
+
 [[package]]
 name = "hashbrown"
 version = "0.14.5"
@@ -649,6 +691,20 @@ dependencies = [
  "hashbrown",
 ]
 
+[[package]]
+name = "heapless"
+version = "0.7.17"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "cdc6457c0eb62c71aac4bc17216026d8410337c4126773b9c5daba343f17964f"
+dependencies = [
+ "atomic-polyfill",
+ "hash32",
+ "rustc_version 0.4.0",
+ "serde",
+ "spin",
+ "stable_deref_trait",
+]
+
 [[package]]
 name = "heck"
 version = "0.5.0"
@@ -1015,7 +1071,7 @@ version = "0.1.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ac8cd24d9f185bb7223958d8c1ff7a961b74b1953fd05dba7cc568a63b3861ec"
 dependencies = [
- "rustc_version",
+ "rustc_version 0.1.7",
 ]
 
 [[package]]
@@ -1171,6 +1227,16 @@ dependencies = [
  "num-traits",
 ]
 
+[[package]]
+name = "num-format"
+version = "0.4.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a652d9771a63711fd3c3deb670acfbe5c30a4072e664d7a3bf5a9e1056ac72c3"
+dependencies = [
+ "arrayvec",
+ "itoa",
+]
+
 [[package]]
 name = "num-integer"
 version = "0.1.46"
@@ -1255,9 +1321,75 @@ dependencies = [
  "uuid",
 ]
 
+[[package]]
+name = "pandora_lib_scan"
+version = "0.1.0"
+source = "git+https://git.t0m4.fr/Thomas/pandora_lib_scan.git#02cf251a4dbb4ed530d10f049902fa041d11e8fe"
+dependencies = [
+ "anyhow",
+ "crossbeam-channel",
+ "env_logger",
+ "flate2",
+ "indicatif",
+ "indicatif-log-bridge",
+ "log",
+ "num-format",
+ "pandora_lib_pileup",
+ "pandora_lib_variants 0.1.0 (git+https://git.t0m4.fr/Thomas/pandora_lib_variants.git)",
+ "postcard",
+ "rayon",
+ "rust-htslib",
+ "serde",
+ "uuid",
+]
+
+[[package]]
+name = "pandora_lib_variants"
+version = "0.1.0"
+dependencies = [
+ "anyhow",
+ "bgzip",
+ "clap",
+ "confy",
+ "crossbeam-deque",
+ "csv",
+ "dashmap",
+ "env_logger",
+ "hashbrown",
+ "indicatif",
+ "indicatif-log-bridge",
+ "log",
+ "noodles-bam",
+ "noodles-bgzf",
+ "noodles-core",
+ "noodles-csi",
+ "noodles-fasta 0.42.0",
+ "noodles-gff",
+ "noodles-sam",
+ "noodles-tabix",
+ "noodles-vcf",
+ "num-integer",
+ "pandora_lib_pileup",
+ "pandora_lib_scan",
+ "pot",
+ "prettytable-rs",
+ "rayon",
+ "regex",
+ "rust-htslib",
+ "rust-lapper",
+ "serde",
+ "serde_json",
+ "serde_rusqlite",
+ "statrs",
+ "trc",
+ "utoipa",
+ "uuid",
+]
+
 [[package]]
 name = "pandora_lib_variants"
 version = "0.1.0"
+source = "git+https://git.t0m4.fr/Thomas/pandora_lib_variants.git#eaefae4807aadf2753973870a555a309176fdf5c"
 dependencies = [
  "anyhow",
  "bgzip",
@@ -1334,6 +1466,18 @@ version = "1.7.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "da544ee218f0d287a911e9c99a39a8c9bc8fcad3cb8db5959940044ecfc67265"
 
+[[package]]
+name = "postcard"
+version = "1.0.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a55c51ee6c0db07e68448e336cf8ea4131a620edefebf9893e759b2d793420f8"
+dependencies = [
+ "cobs",
+ "embedded-io",
+ "heapless",
+ "serde",
+]
+
 [[package]]
 name = "pot"
 version = "3.0.0"
@@ -1588,7 +1732,16 @@ version = "0.1.7"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "c5f5376ea5e30ce23c03eb77cbe4962b988deead10910c372b226388b594c084"
 dependencies = [
- "semver",
+ "semver 0.1.20",
+]
+
+[[package]]
+name = "rustc_version"
+version = "0.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bfa0f585226d2e68097d4f95d113b15b83a82e819ab25717ec0590d9584ef366"
+dependencies = [
+ "semver 1.0.23",
 ]
 
 [[package]]
@@ -1624,6 +1777,12 @@ version = "0.1.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "d4f410fedcf71af0345d7607d246e7ad15faaadd49d240ee3b24e5dc21a820ac"
 
+[[package]]
+name = "semver"
+version = "1.0.23"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "61697e0a1c7e512e84a621326239844a24d8207b4669b41bc18b32ea5cbf988b"
+
 [[package]]
 name = "serde"
 version = "1.0.205"
@@ -1700,6 +1859,15 @@ version = "1.13.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67"
 
+[[package]]
+name = "spin"
+version = "0.9.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6980e8d7511241f8acf4aebddbb1ff938df5eebe98691418c4468d0b72a96a67"
+dependencies = [
+ "lock_api",
+]
+
 [[package]]
 name = "stable_deref_trait"
 version = "1.2.0"

Cargo.toml

@@ -42,4 +42,5 @@ trc = "1.2.4"
 pot = "=3.0.0"
 utoipa = "4.2.3"
 regex = "1.10.6"
+pandora_lib_scan = { git  = "https://git.t0m4.fr/Thomas/pandora_lib_scan.git" }
 pandora_lib_pileup = { git  = "https://git.t0m4.fr/Thomas/pandora_lib_pileup.git" }

src/variants.rs

@@ -854,6 +854,7 @@ impl Variants {
                             &v.contig,
                             v.position as i32,
                             false,
+                            50,
                         )
                         .unwrap()
                         .iter()
@@ -866,6 +867,7 @@ impl Variants {
                         &v.contig,
                         v.position as i32,
                         true,
+                        50,
                     )
                     .unwrap()
                     .iter()
@@ -877,6 +879,7 @@ impl Variants {
                         &v.contig,
                         v.position as i32,
                         false,
+                        50,
                     )
                     .unwrap()
                     .iter()