bams

Cargo.lock

@@ -2,6 +2,21 @@
 # It is not intended for manual editing.
 version = 3
 
+[[package]]
+name = "addr2line"
+version = "0.22.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "6e4503c46a5c0c7844e948c9a4d6acd9f50cccb4de1c48eb9e291ea17470c678"
+dependencies = [
+ "gimli",
+]
+
+[[package]]
+name = "adler"
+version = "1.0.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe"
+
 [[package]]
 name = "ahash"
 version = "0.8.11"
@@ -76,7 +91,7 @@ version = "1.1.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "ad186efb764318d35165f1758e7dcef3b10628e26d41a44bc5550652e6804391"
 dependencies = [
- "windows-sys",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
@@ -86,7 +101,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "61a38449feb7068f52bb06c12759005cf459ee52bb4adc1d5a7c4322d716fb19"
 dependencies = [
  "anstyle",
- "windows-sys",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
@@ -549,6 +564,21 @@ dependencies = [
  "num-traits",
 ]
 
+[[package]]
+name = "backtrace"
+version = "0.3.73"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5cc23269a4f8976d0a4d2e7109211a419fe30e8d88d677cd60b6bc79c5732e0a"
+dependencies = [
+ "addr2line",
+ "cc",
+ "cfg-if",
+ "libc",
+ "miniz_oxide",
+ "object",
+ "rustc-demangle",
+]
+
 [[package]]
 name = "base64"
 version = "0.21.7"
@@ -672,7 +702,7 @@ dependencies = [
  "js-sys",
  "num-traits",
  "wasm-bindgen",
- "windows-targets",
+ "windows-targets 0.52.6",
 ]
 
 [[package]]
@@ -701,6 +731,19 @@ version = "1.0.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0b6a852b24ab71dffc585bcb46eaf7959d175cb865a7152e35b348d1b2960422"
 
+[[package]]
+name = "console"
+version = "0.15.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0e1f83fc076bd6dd27517eacdf25fef6c4dfe5f1d7448bafaaf3a26f13b5e4eb"
+dependencies = [
+ "encode_unicode",
+ "lazy_static",
+ "libc",
+ "unicode-width",
+ "windows-sys 0.52.0",
+]
+
 [[package]]
 name = "const-random"
 version = "0.1.18"
@@ -791,7 +834,7 @@ dependencies = [
  "openssl-sys",
  "pkg-config",
  "vcpkg",
- "windows-sys",
+ "windows-sys 0.52.0",
 ]
 
 [[package]]
@@ -837,6 +880,12 @@ version = "1.13.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "60b1af1c220855b6ceac025d3f6ecdd2b7c4894bfe9cd9bda4fbb4bc7c0d4cf0"
 
+[[package]]
+name = "encode_unicode"
+version = "0.3.6"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a357d28ed41a50f9c765dbfe56cbc04a64e53e5fc58ba79fbc34c10ef3df831f"
+
 [[package]]
 name = "env_filter"
 version = "0.1.0"
@@ -847,6 +896,19 @@ dependencies = [
  "regex",
 ]
 
+[[package]]
+name = "env_logger"
+version = "0.10.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4cd405aab171cb85d6735e5c8d9db038c17d3ca007a4d2c25f337935c3d90580"
+dependencies = [
+ "humantime",
+ "is-terminal",
+ "log",
+ "regex",
+ "termcolor",
+]
+
 [[package]]
 name = "env_logger"
 version = "0.11.3"
@@ -910,6 +972,95 @@ dependencies = [
  "quick-error",
 ]
 
+[[package]]
+name = "futures"
+version = "0.3.30"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "645c6916888f6cb6350d2550b80fb63e734897a8498abe35cfb732b6487804b0"
+dependencies = [
+ "futures-channel",
+ "futures-core",
+ "futures-executor",
+ "futures-io",
+ "futures-sink",
+ "futures-task",
+ "futures-util",
+]
+
+[[package]]
+name = "futures-channel"
+version = "0.3.30"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "eac8f7d7865dcb88bd4373ab671c8cf4508703796caa2b1985a9ca867b3fcb78"
+dependencies = [
+ "futures-core",
+ "futures-sink",
+]
+
+[[package]]
+name = "futures-core"
+version = "0.3.30"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "dfc6580bb841c5a68e9ef15c77ccc837b40a7504914d52e47b8b0e9bbda25a1d"
+
+[[package]]
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+version = "0.3.30"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a576fc72ae164fca6b9db127eaa9a9dda0d61316034f33a0a0d4eda41f02b01d"
+dependencies = [
+ "futures-core",
+ "futures-task",
+ "futures-util",
+]
+
+[[package]]
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+version = "0.3.30"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a44623e20b9681a318efdd71c299b6b222ed6f231972bfe2f224ebad6311f0c1"
+
+[[package]]
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+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "87750cf4b7a4c0625b1529e4c543c2182106e4dedc60a2a6455e00d212c489ac"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.71",
+]
+
+[[package]]
+name = "futures-sink"
+version = "0.3.30"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9fb8e00e87438d937621c1c6269e53f536c14d3fbd6a042bb24879e57d474fb5"
+
+[[package]]
+name = "futures-task"
+version = "0.3.30"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "38d84fa142264698cdce1a9f9172cf383a0c82de1bddcf3092901442c4097004"
+
+[[package]]
+name = "futures-util"
+version = "0.3.30"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3d6401deb83407ab3da39eba7e33987a73c3df0c82b4bb5813ee871c19c41d48"
+dependencies = [
+ "futures-channel",
+ "futures-core",
+ "futures-io",
+ "futures-macro",
+ "futures-sink",
+ "futures-task",
+ "memchr",
+ "pin-project-lite",
+ "pin-utils",
+ "slab",
+]
+
 [[package]]
 name = "getrandom"
 version = "0.2.15"
@@ -921,6 +1072,12 @@ dependencies = [
  "wasi",
 ]
 
+[[package]]
+name = "gimli"
+version = "0.29.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "40ecd4077b5ae9fd2e9e169b102c6c330d0605168eb0e8bf79952b256dbefffd"
+
 [[package]]
 name = "glob"
 version = "0.3.1"
@@ -950,6 +1107,12 @@ version = "0.5.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "2304e00983f87ffb38b55b444b5e3b60a884b5d30c0fca7d82fe33449bbe55ea"
 
+[[package]]
+name = "hermit-abi"
+version = "0.3.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "d231dfb89cfffdbc30e7fc41579ed6066ad03abda9e567ccafae602b97ec5024"
+
 [[package]]
 name = "hts-sys"
 version = "2.1.4"
@@ -1022,6 +1185,39 @@ dependencies = [
  "hashbrown",
 ]
 
+[[package]]
+name = "indicatif"
+version = "0.17.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "763a5a8f45087d6bcea4222e7b72c291a054edf80e4ef6efd2a4979878c7bea3"
+dependencies = [
+ "console",
+ "instant",
+ "number_prefix",
+ "portable-atomic",
+ "unicode-width",
+]
+
+[[package]]
+name = "instant"
+version = "0.1.13"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "e0242819d153cba4b4b05a5a8f2a7e9bbf97b6055b2a002b395c96b5ff3c0222"
+dependencies = [
+ "cfg-if",
+]
+
+[[package]]
+name = "is-terminal"
+version = "0.4.12"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f23ff5ef2b80d608d61efee834934d862cd92461afc0560dedf493e4c033738b"
+dependencies = [
+ "hermit-abi",
+ "libc",
+ "windows-sys 0.52.0",
+]
+
 [[package]]
 name = "is_terminal_polyfill"
 version = "1.70.0"
@@ -1150,7 +1346,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e310b3a6b5907f99202fcdb4960ff45b93735d7c7d96b760fcff8db2dc0e103d"
 dependencies = [
  "cfg-if",
- "windows-targets",
+ "windows-targets 0.52.6",
 ]
 
 [[package]]
@@ -1178,6 +1374,16 @@ version = "1.2.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "bfae20f6b19ad527b550c223fddc3077a547fc70cda94b9b566575423fd303ee"
 
+[[package]]
+name = "lock_api"
+version = "0.4.12"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "07af8b9cdd281b7915f413fa73f29ebd5d55d0d3f0155584dade1ff18cea1b17"
+dependencies = [
+ "autocfg",
+ "scopeguard",
+]
+
 [[package]]
 name = "log"
 version = "0.4.22"
@@ -1207,6 +1413,26 @@ version = "0.2.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "68354c5c6bd36d73ff3feceb05efa59b6acb7626617f4962be322a825e61f79a"
 
+[[package]]
+name = "miniz_oxide"
+version = "0.7.4"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "b8a240ddb74feaf34a79a7add65a741f3167852fba007066dcac1ca548d89c08"
+dependencies = [
+ "adler",
+]
+
+[[package]]
+name = "mio"
+version = "0.8.11"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a4a650543ca06a924e8b371db273b2756685faae30f8487da1b56505a8f78b0c"
+dependencies = [
+ "libc",
+ "wasi",
+ "windows-sys 0.48.0",
+]
+
 [[package]]
 name = "newtype_derive"
 version = "0.1.6"
@@ -1300,6 +1526,31 @@ dependencies = [
  "libm",
 ]
 
+[[package]]
+name = "num_cpus"
+version = "1.16.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4161fcb6d602d4d2081af7c3a45852d875a03dd337a6bfdd6e06407b61342a43"
+dependencies = [
+ "hermit-abi",
+ "libc",
+]
+
+[[package]]
+name = "number_prefix"
+version = "0.4.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "830b246a0e5f20af87141b25c173cd1b609bd7779a4617d6ec582abaf90870f3"
+
+[[package]]
+name = "object"
+version = "0.36.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "081b846d1d56ddfc18fdf1a922e4f6e07a11768ea1b92dec44e42b72712ccfce"
+dependencies = [
+ "memchr",
+]
+
 [[package]]
 name = "once_cell"
 version = "1.19.0"
@@ -1328,6 +1579,21 @@ dependencies = [
  "vcpkg",
 ]
 
+[[package]]
+name = "pandora_lib_bindings"
+version = "0.1.0"
+source = "git+https://git.t0m4.fr/Thomas/pandora_lib_bindings.git#f89f9705d63ee9cdab5b5b1d81b2f351d0ce5b77"
+dependencies = [
+ "anyhow",
+ "env_logger 0.10.2",
+ "futures",
+ "indicatif",
+ "log",
+ "regex",
+ "tokio",
+ "uuid",
+]
+
 [[package]]
 name = "pandora_lib_pileup"
 version = "0.1.0"
@@ -1335,7 +1601,7 @@ source = "git+https://git.t0m4.fr/Thomas/pandora_lib_pileup.git#869e07f8d4dca917
 dependencies = [
  "anyhow",
  "average",
- "env_logger",
+ "env_logger 0.11.3",
  "log",
  "rayon",
  "rust-htslib",
@@ -1358,21 +1624,57 @@ dependencies = [
  "anyhow",
  "chrono",
  "csv",
- "env_logger",
+ "env_logger 0.11.3",
  "glob",
  "log",
+ "pandora_lib_bindings",
  "pandora_lib_pileup",
  "pandora_lib_pod5",
  "regex",
  "serde",
 ]
 
+[[package]]
+name = "parking_lot"
+version = "0.12.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "f1bf18183cf54e8d6059647fc3063646a1801cf30896933ec2311622cc4b9a27"
+dependencies = [
+ "lock_api",
+ "parking_lot_core",
+]
+
+[[package]]
+name = "parking_lot_core"
+version = "0.9.10"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "1e401f977ab385c9e4e3ab30627d6f26d00e2c73eef317493c4ec6d468726cf8"
+dependencies = [
+ "cfg-if",
+ "libc",
+ "redox_syscall",
+ "smallvec",
+ "windows-targets 0.52.6",
+]
+
 [[package]]
 name = "percent-encoding"
 version = "2.3.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "e3148f5046208a5d56bcfc03053e3ca6334e51da8dfb19b6cdc8b306fae3283e"
 
+[[package]]
+name = "pin-project-lite"
+version = "0.2.14"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "bda66fc9667c18cb2758a2ac84d1167245054bcf85d5d1aaa6923f45801bdd02"
+
+[[package]]
+name = "pin-utils"
+version = "0.1.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8b870d8c151b6f2fb93e84a13146138f05d02ed11c7e7c54f8826aaaf7c9f184"
+
 [[package]]
 name = "pkg-config"
 version = "0.3.30"
@@ -1391,6 +1693,12 @@ dependencies = [
  "uuid",
 ]
 
+[[package]]
+name = "portable-atomic"
+version = "1.6.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "7170ef9988bc169ba16dd36a7fa041e5c4cbeb6a35b76d4c03daded371eae7c0"
+
 [[package]]
 name = "proc-macro2"
 version = "1.0.86"
@@ -1435,6 +1743,15 @@ dependencies = [
  "crossbeam-utils",
 ]
 
+[[package]]
+name = "redox_syscall"
+version = "0.5.3"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2a908a6e00f1fdd0dfd9c0eb08ce85126f6d8bbda50017e74bc4a4b7d4a926a4"
+dependencies = [
+ "bitflags 2.6.0",
+]
+
 [[package]]
 name = "regex"
 version = "1.10.5"
@@ -1486,6 +1803,12 @@ dependencies = [
  "url",
 ]
 
+[[package]]
+name = "rustc-demangle"
+version = "0.1.24"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "719b953e2095829ee67db738b3bfa9fa368c94900df327b3f07fe6e794d2fe1f"
+
 [[package]]
 name = "rustc-hash"
 version = "1.1.0"
@@ -1522,6 +1845,12 @@ version = "1.0.18"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "f3cb5ba0dc43242ce17de99c180e96db90b235b8a9fdc9543c96d2209116bd9f"
 
+[[package]]
+name = "scopeguard"
+version = "1.2.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49"
+
 [[package]]
 name = "semver"
 version = "0.1.20"
@@ -1571,6 +1900,40 @@ version = "1.3.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0fda2ff0d084019ba4d7c6f371c95d8fd75ce3524c3cb8fb653a3023f6323e64"
 
+[[package]]
+name = "signal-hook-registry"
+version = "1.4.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a9e9e0b4211b72e7b8b6e85c807d36c212bdb33ea8587f7569562a84df5465b1"
+dependencies = [
+ "libc",
+]
+
+[[package]]
+name = "slab"
+version = "0.4.9"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8f92a496fb766b417c996b9c5e57daf2f7ad3b0bebe1ccfca4856390e3d3bb67"
+dependencies = [
+ "autocfg",
+]
+
+[[package]]
+name = "smallvec"
+version = "1.13.2"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "3c5e1a9a646d36c3599cd173a41282daf47c44583ad367b8e6837255952e5c67"
+
+[[package]]
+name = "socket2"
+version = "0.5.7"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ce305eb0b4296696835b71df73eb912e0f1ffd2556a501fcede6e0c50349191c"
+dependencies = [
+ "libc",
+ "windows-sys 0.52.0",
+]
+
 [[package]]
 name = "static_assertions"
 version = "1.1.0"
@@ -1612,6 +1975,15 @@ dependencies = [
  "unicode-ident",
 ]
 
+[[package]]
+name = "termcolor"
+version = "1.4.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "06794f8f6c5c898b3275aebefa6b8a1cb24cd2c6c79397ab15774837a0bc5755"
+dependencies = [
+ "winapi-util",
+]
+
 [[package]]
 name = "thiserror"
 version = "1.0.62"
@@ -1656,6 +2028,36 @@ version = "0.1.1"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "1f3ccbac311fea05f86f61904b462b55fb3df8837a366dfc601a0161d0532f20"
 
+[[package]]
+name = "tokio"
+version = "1.38.1"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "eb2caba9f80616f438e09748d5acda951967e1ea58508ef53d9c6402485a46df"
+dependencies = [
+ "backtrace",
+ "bytes",
+ "libc",
+ "mio",
+ "num_cpus",
+ "parking_lot",
+ "pin-project-lite",
+ "signal-hook-registry",
+ "socket2",
+ "tokio-macros",
+ "windows-sys 0.48.0",
+]
+
+[[package]]
+name = "tokio-macros"
+version = "2.3.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "5f5ae998a069d4b5aba8ee9dad856af7d520c3699e6159b185c2acd48155d39a"
+dependencies = [
+ "proc-macro2",
+ "quote",
+ "syn 2.0.71",
+]
+
 [[package]]
 name = "unicode-bidi"
 version = "0.3.15"
@@ -1677,6 +2079,12 @@ dependencies = [
  "tinyvec",
 ]
 
+[[package]]
+name = "unicode-width"
+version = "0.1.13"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0336d538f7abc86d282a4189614dfaa90810dfc2c6f6427eaf88e16311dd225d"
+
 [[package]]
 name = "url"
 version = "2.5.2"
@@ -1701,6 +2109,7 @@ source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "81dfa00651efa65069b0b6b651f4aaa31ba9e3c3ce0137aaad053604ee7e0314"
 dependencies = [
  "getrandom",
+ "serde",
 ]
 
 [[package]]
@@ -1775,13 +2184,31 @@ version = "0.2.92"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "af190c94f2773fdb3729c55b007a722abb5384da03bc0986df4c289bf5567e96"
 
+[[package]]
+name = "winapi-util"
+version = "0.1.8"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "4d4cc384e1e73b93bafa6fb4f1df8c41695c8a91cf9c4c64358067d15a7b6c6b"
+dependencies = [
+ "windows-sys 0.52.0",
+]
+
 [[package]]
 name = "windows-core"
 version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "33ab640c8d7e35bf8ba19b884ba838ceb4fba93a4e8c65a9059d08afcfc683d9"
 dependencies = [
- "windows-targets",
+ "windows-targets 0.52.6",
+]
+
+[[package]]
+name = "windows-sys"
+version = "0.48.0"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9"
+dependencies = [
+ "windows-targets 0.48.5",
 ]
 
 [[package]]
@@ -1790,7 +2217,22 @@ version = "0.52.0"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d"
 dependencies = [
- "windows-targets",
+ "windows-targets 0.52.6",
+]
+
+[[package]]
+name = "windows-targets"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c"
+dependencies = [
+ "windows_aarch64_gnullvm 0.48.5",
+ "windows_aarch64_msvc 0.48.5",
+ "windows_i686_gnu 0.48.5",
+ "windows_i686_msvc 0.48.5",
+ "windows_x86_64_gnu 0.48.5",
+ "windows_x86_64_gnullvm 0.48.5",
+ "windows_x86_64_msvc 0.48.5",
 ]
 
 [[package]]
@@ -1799,28 +2241,46 @@ version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973"
 dependencies = [
- "windows_aarch64_gnullvm",
- "windows_aarch64_msvc",
- "windows_i686_gnu",
+ "windows_aarch64_gnullvm 0.52.6",
+ "windows_aarch64_msvc 0.52.6",
+ "windows_i686_gnu 0.52.6",
  "windows_i686_gnullvm",
- "windows_i686_msvc",
- "windows_x86_64_gnu",
- "windows_x86_64_gnullvm",
- "windows_x86_64_msvc",
+ "windows_i686_msvc 0.52.6",
+ "windows_x86_64_gnu 0.52.6",
+ "windows_x86_64_gnullvm 0.52.6",
+ "windows_x86_64_msvc 0.52.6",
 ]
 
+[[package]]
+name = "windows_aarch64_gnullvm"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8"
+
 [[package]]
 name = "windows_aarch64_gnullvm"
 version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3"
 
+[[package]]
+name = "windows_aarch64_msvc"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc"
+
 [[package]]
 name = "windows_aarch64_msvc"
 version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469"
 
+[[package]]
+name = "windows_i686_gnu"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e"
+
 [[package]]
 name = "windows_i686_gnu"
 version = "0.52.6"
@@ -1833,24 +2293,48 @@ version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66"
 
+[[package]]
+name = "windows_i686_msvc"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406"
+
 [[package]]
 name = "windows_i686_msvc"
 version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66"
 
+[[package]]
+name = "windows_x86_64_gnu"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e"
+
 [[package]]
 name = "windows_x86_64_gnu"
 version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78"
 
+[[package]]
+name = "windows_x86_64_gnullvm"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc"
+
 [[package]]
 name = "windows_x86_64_gnullvm"
 version = "0.52.6"
 source = "registry+https://github.com/rust-lang/crates.io-index"
 checksum = "24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d"
 
+[[package]]
+name = "windows_x86_64_msvc"
+version = "0.48.5"
+source = "registry+https://github.com/rust-lang/crates.io-index"
+checksum = "ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538"
+
 [[package]]
 name = "windows_x86_64_msvc"
 version = "0.52.6"

Cargo.toml

@@ -10,6 +10,7 @@ anyhow = "1.0.86"
 glob = "0.3.1"
 pandora_lib_pod5 = { git = "https://git.t0m4.fr/Thomas/pandora_lib_pod5.git" }
 pandora_lib_pileup = { git = "https://git.t0m4.fr/Thomas/pandora_lib_pileup.git" }
+pandora_lib_bindings = { git = "https://git.t0m4.fr/Thomas/pandora_lib_bindings.git" }
 regex = "1.10.5"
 chrono = "0.4.38"
 csv = "1.3.0"

src/bam.rs

@@ -0,0 +1,70 @@
+use std::{
+    fs::{self, Metadata},
+    path::PathBuf,
+    str::FromStr,
+};
+
+use anyhow::{anyhow, Context};
+use pandora_lib_bindings::{
+    progs::cramino::{Cramino, CraminoRes},
+    utils::RunBin,
+};
+
+#[derive(Debug)]
+pub struct Bam {
+    pub id: String,
+    pub time_point: String,
+    pub path: PathBuf,
+    pub file_metadata: Metadata,
+    pub cramino: CraminoRes,
+}
+
+impl Bam {
+    pub fn new(bam_dir: &str, id: &str, time_point: &str) -> anyhow::Result<Self> {
+        let bam_path = format!("{bam_dir}/{id}/{time_point}/{id}_{time_point}_hs1.bam");
+        let path = PathBuf::from_str(&bam_path)?;
+        if !path.exists() {
+            return Err(anyhow!("Bam file missing {bam_path}"));
+        }
+
+        let tp_dir = path.parent().context("Can't parse parent from: {bam_path}")?;
+        let cramino_path = format!("{}/{id}_{time_point}_hs1_cramino.txt", tp_dir.to_string_lossy());
+        let file_metadata = fs::metadata(&path)?;
+        if !PathBuf::from_str(&cramino_path)?.exists() {
+            return Err(anyhow!("Cramino file missing {cramino_path}"));
+        }
+        let mut cramino = Cramino::default().with_result_path(&cramino_path);
+        cramino.parse_results()?;
+
+        if let Some(cramino) = cramino.results {
+            Ok(Self {
+                path,
+                file_metadata,
+                cramino,
+                id: id.to_string(),
+                time_point: time_point.to_string(),
+            })
+        } else {
+            Err(anyhow!("Cramino results parsing failed"))
+        }
+    }
+}
+
+#[derive(Debug)]
+pub struct BamCollection {
+    pub bams: Vec<Bam>,
+}
+
+pub fn load_bam_collection(ids: Vec<String>, bam_dir: &str, time_points: Vec<&str>) -> BamCollection {
+    let mut bams = Vec::new();
+
+    for id in ids {
+        for tp in time_points.iter() {
+            if let std::result::Result::Ok(bam) = Bam::new(bam_dir, &id,tp) {
+                bams.push(bam);
+            }
+        }
+    }
+
+    BamCollection { bams }
+}

src/lib.rs

@@ -1,10 +1,11 @@
+pub mod bam;
 pub mod dorado;
 pub mod modkit;
 pub mod pod5;
 
 #[cfg(test)]
 mod tests {
-    use self::{dorado::Run, pod5::Runs};
+    use self::{bam::Bam, dorado::Run, pod5::Runs};
     use super::*;
 
     #[test]
@@ -69,4 +70,11 @@ mod tests {
         runs.fc_done();
         Ok(())
     }
+
+    #[test]
+    fn bam() -> anyhow::Result<()> {
+        // let bam_collection = ;
+        // println!("{bam:#?}");
+        Ok(())
+    }
 }

src/pod5.rs

@@ -423,6 +423,7 @@ impl Runs {
                                     let mut pod_dir = PathBuf::from(pod_dir);
                                     pod_dir.pop();
 
+                                    // TODO sheduler
                                     println!(
                                         "complete_bam.sh {} {} {}",
                                         c.id,