ser

Cargo.lock

@@ -86,9 +86,9 @@ dependencies = [
 
 [[package]]
 name = "anyhow"
-version = "1.0.83"
+version = "1.0.86"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "25bdb32cbbdce2b519a9cd7df3a678443100e265d5e25ca763b7572a5104f5f3"
+checksum = "b3d1d046238990b9cf5bcde22a3fb3584ee5cf65fb2765f454ed428c7a0063da"
 
 [[package]]
 name = "approx"
@@ -184,9 +184,9 @@ dependencies = [
 
 [[package]]
 name = "cc"
-version = "1.0.97"
+version = "1.0.98"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "099a5357d84c4c61eb35fc8eafa9a79a902c2f76911e5747ced4e032edd8d9b4"
+checksum = "41c270e7540d725e65ac7f1b212ac8ce349719624d7bcff99f8e2e488e8cf03f"
 dependencies = [
  "jobserver",
  "libc",
@@ -230,7 +230,7 @@ dependencies = [
  "heck 0.5.0",
  "proc-macro2",
  "quote",
- "syn 2.0.64",
+ "syn 2.0.65",
 ]
 
 [[package]]
@@ -281,9 +281,9 @@ dependencies = [
 
 [[package]]
 name = "crc32fast"
-version = "1.4.0"
+version = "1.4.2"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "b3855a8a784b474f333699ef2bbca9db2c4a1f6d9088a90a2d25b1eb53111eaa"
+checksum = "a97769d94ddab943e4510d138150169a2758b5ef3eb191a9ee688de3e23ef7b3"
 dependencies = [
  "cfg-if",
 ]
@@ -303,9 +303,9 @@ dependencies = [
 
 [[package]]
 name = "crossbeam-channel"
-version = "0.5.12"
+version = "0.5.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "ab3db02a9c5b5121e1e42fbdb1aeb65f5e02624cc58c43f2884c6ccac0b82f95"
+checksum = "33480d6946193aa8033910124896ca395333cae7e2d1113d1fef6c3272217df2"
 dependencies = [
  "crossbeam-utils",
 ]
@@ -340,9 +340,9 @@ dependencies = [
 
 [[package]]
 name = "crossbeam-utils"
-version = "0.8.19"
+version = "0.8.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "248e3bacc7dc6baa3b21e405ee045c3047101a49145e7e9eca583ab4c2ca5345"
+checksum = "22ec99545bb0ed0ea7bb9b8e1e9122ea386ff8a48c0922e43f36d45ab09e0e80"
 
 [[package]]
 name = "crunchy"
@@ -553,9 +553,9 @@ dependencies = [
 
 [[package]]
 name = "getrandom"
-version = "0.2.14"
+version = "0.2.15"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "94b22e06ecb0110981051723910cbf0b5f5e09a2062dd7663334ee79a9d1286c"
+checksum = "c4567c8db10ae91089c99af84c68c38da3ec2f087c3f82960bcdbf3656b6f4d7"
 dependencies = [
  "cfg-if",
  "libc",
@@ -691,9 +691,9 @@ dependencies = [
 
 [[package]]
 name = "instant"
-version = "0.1.12"
+version = "0.1.13"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7a5bbe824c507c5da5956355e86a746d82e0e1464f65d862cc5e71da70e94b2c"
+checksum = "e0242819d153cba4b4b05a5a8f2a7e9bbf97b6055b2a002b395c96b5ff3c0222"
 dependencies = [
  "cfg-if",
 ]
@@ -811,9 +811,9 @@ dependencies = [
 
 [[package]]
 name = "libc"
-version = "0.2.153"
+version = "0.2.155"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9c198f91728a82281a64e1f4f9eeb25d82cb32a5de251c6bd1b5154d63a8e7bd"
+checksum = "97b3888a4aecf77e811145cadf6eef5901f4782c53886191b2f693f24761847c"
 
 [[package]]
 name = "libm"
@@ -905,9 +905,9 @@ checksum = "6c8640c5d730cb13ebd907d8d04b52f55ac9a2eec55b440c8892f40d56c76c1d"
 
 [[package]]
 name = "miniz_oxide"
-version = "0.7.2"
+version = "0.7.3"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "9d811f3e15f28568be3407c8e7fdb6514c1cda3cb30683f15b6a1a1dc4ea14a7"
+checksum = "87dfd01fe195c66b572b37921ad8803d010623c0aca821bea2302239d155cdae"
 dependencies = [
  "adler",
 ]
@@ -1214,7 +1214,7 @@ dependencies = [
 [[package]]
 name = "pandora_lib_variants"
 version = "0.1.0"
-source = "git+https://git.t0m4.fr/Thomas/pandora_lib_variants.git#53cbd13629ece9d4612dffd2a58d8c4f208b5fbf"
+source = "git+https://git.t0m4.fr/Thomas/pandora_lib_variants.git#50f254410e8e5e50b1f8203754e9b71381733b33"
 dependencies = [
  "anyhow",
  "bgzip",
@@ -1321,9 +1321,9 @@ dependencies = [
 
 [[package]]
 name = "proc-macro2"
-version = "1.0.82"
+version = "1.0.83"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "8ad3d49ab951a01fbaafe34f2ec74122942fe18a3f9814c3268f1bb72042131b"
+checksum = "0b33eb56c327dec362a9e55b3ad14f9d2f0904fb5a5b03b513ab5465399e9f43"
 dependencies = [
  "unicode-ident",
 ]
@@ -1583,7 +1583,7 @@ checksum = "6048858004bcff69094cd972ed40a32500f153bd3be9f716b2eed2e8217c4838"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.64",
+ "syn 2.0.65",
 ]
 
 [[package]]
@@ -1667,7 +1667,7 @@ dependencies = [
  "proc-macro2",
  "quote",
  "rustversion",
- "syn 2.0.64",
+ "syn 2.0.65",
 ]
 
 [[package]]
@@ -1683,9 +1683,9 @@ dependencies = [
 
 [[package]]
 name = "syn"
-version = "2.0.64"
+version = "2.0.65"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "7ad3dee41f36859875573074334c200d1add8e4a87bb37113ebd31d926b7b11f"
+checksum = "d2863d96a84c6439701d7a38f9de935ec562c8832cc55d1dde0f513b52fad106"
 dependencies = [
  "proc-macro2",
  "quote",
@@ -1714,22 +1714,22 @@ dependencies = [
 
 [[package]]
 name = "thiserror"
-version = "1.0.60"
+version = "1.0.61"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "579e9083ca58dd9dcf91a9923bb9054071b9ebbd800b342194c9feb0ee89fc18"
+checksum = "c546c80d6be4bc6a00c0f01730c08df82eaa7a7a61f11d656526506112cc1709"
 dependencies = [
  "thiserror-impl",
 ]
 
 [[package]]
 name = "thiserror-impl"
-version = "1.0.60"
+version = "1.0.61"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "e2470041c06ec3ac1ab38d0356a6119054dedaea53e12fbefc0de730a1c08524"
+checksum = "46c3384250002a6d5af4d114f2845d37b57521033f30d5c3f46c4d70e1197533"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.64",
+ "syn 2.0.65",
 ]
 
 [[package]]
@@ -1846,9 +1846,9 @@ checksum = "9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423"
 
 [[package]]
 name = "wide"
-version = "0.7.19"
+version = "0.7.20"
 source = "registry+https://github.com/rust-lang/crates.io-index"
-checksum = "aab6594190de06d718a5dbc5fa781ab62f8903797056480e549ca74add6b7065"
+checksum = "21e005a4cc35784183a9e39cb22e9a9c46353ef6a7f113fd8d36ddc58c15ef3c"
 dependencies = [
  "bytemuck",
  "safe_arch",
@@ -1975,5 +1975,5 @@ checksum = "15e934569e47891f7d9411f1a451d947a60e000ab3bd24fbb970f000387d1b3b"
 dependencies = [
  "proc-macro2",
  "quote",
- "syn 2.0.64",
+ "syn 2.0.65",
 ]

src/bam.rs

@@ -3,14 +3,15 @@ use itertools::Itertools;
 
 use anyhow::{Context, Error, Ok, Result, anyhow};
 use rust_htslib::{bam, bam::Read};
+use serde::Serialize;
 
-#[derive(Debug, Clone)]
+#[derive(Debug, Clone, Serialize)]
 pub struct Bam {
     pub path: PathBuf,
     pub origin: BamOrigin,
 }
 
-#[derive(Debug, Clone)]
+#[derive(Debug, Clone, Serialize)]
 pub enum BamOrigin {
     DIAG,
     MRD,

src/cases.rs

@@ -11,6 +11,7 @@ use pandora_lib_pileup::get_hts_nt_pileup;
 use pandora_lib_stats::chi_square_test_for_proportions;
 use pandora_lib_variants::variants::*;
 use rayon::prelude::*;
+use serde::Serialize;
 use std::{
     collections::HashMap,
     io::{BufRead, BufReader},
@@ -21,7 +22,7 @@ use std::{
 use rand::seq::IteratorRandom;
 use rust_htslib::bam;
 
-#[derive(Debug, Clone)]
+#[derive(Debug, Clone, Serialize)]
 pub struct Cases {
     pub cases: Vec<Case>,
     pub config: Config,
@@ -121,7 +122,7 @@ impl DerefMut for Cases {
     }
 }
 
-#[derive(Debug, Clone)]
+#[derive(Debug, Clone, Serialize)]
 pub struct Case {
     pub id: String,
     pub diag_bam: Bam,