clean up json handling (#390)

* Replaces all custom JSON parsing code with serde.
* Adds a dependency on martian-filetypes for lazy JSON loading.
* Inverts control flows to return values instead of mutating collections provided by arguments.

deny.toml

@@ -130,6 +130,7 @@ allow-registry = ["https://github.com/rust-lang/crates.io-index"]
 allow-git = [
     # TODO: remove this
     "https://github.com/Barandis/qd",
+    "https://github.com/martian-lang/martian-rust",
 ]
 
 [sources.allow-org]
@@ -139,3 +140,9 @@ github = ["10XGenomics"]
 gitlab = []
 # 1 or more bitbucket.org organizations to allow git sources for
 bitbucket = []
+
+
+[[bans.skip]]
+# many packages depend on syn 1
+name = "syn"
+version = "1.0.105"

enclone_args/Cargo.toml

@@ -30,12 +30,14 @@ evalexpr = ">=7, <12"
 expr_tools = { path = "../expr_tools" }
 io_utils = { path = "../io_utils" }
 itertools.workspace = true
+martian-filetypes = { git = "https://github.com/martian-lang/martian-rust", branch = "master" }
 rand = "0.8"
 rayon = "1"
 regex = { version = "1", default-features = false, features = ["std", "perf"] }
 serde_json = "1"
 string_utils = { path = "../string_utils" }
 vdj_ann = { path = "../vdj_ann" }
+vdj_types = { path = "../vdj_types" }
 vector_utils = { path = "../vector_utils" }
 
 [target.'cfg(not(windows))'.dependencies.hdf5]