Feat/export info as json

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "bqtools"
-version = "0.5.5"
+version = "0.5.6"
 edition = "2021"
 license = "MIT"
 authors = ["Noam Teyssier <noam.teyssier@arcinstitute.org>"]
@@ -31,6 +31,8 @@ rand = "0.10.0"
 regex = "1.12.2"
 sassy = { version = "0.2.1", optional = true }
 serde = { version = "1.0.228", features = ["derive"] }
+serde_json = "1.0.149"
+thousands = "0.2.0"
 walkdir = "2.5.0"
 zstd = { version = "0.13.3", features = ["zstdmt"] }
 

README.md

@@ -266,8 +266,14 @@ bqtools info input.vbq --show-index
 
 # print out the CBQ block headers
 bqtools info input.cbq --show-headers
+
+# export as json
+bqtools info input.cbq --json
 ```
 
+> Note: using `info` without the `--json` flag will format the number of records to include underscores to delimit the thousands.
+> To avoid this behavior or to pass raw numerical values forward use the `--json` flag.
+
 ### Grep
 
 You can easily search for specific subsequences or regular expressions within BINSEQ files:

src/cli/info.rs

@@ -1,12 +1,10 @@
 use clap::Parser;
 
-use super::InputBinseq;
-
 #[derive(Parser, Debug)]
 /// Show information about a BINSEQ file.
 pub struct InfoCommand {
-    #[clap(flatten)]
-    pub input: InputBinseq,
+    #[clap(num_args=1.., required=true)]
+    pub input: Vec<String>,
 
     #[clap(flatten)]
     pub opts: InfoOpts,
@@ -16,14 +14,18 @@ pub struct InfoCommand {
 #[clap(next_help_heading = "INFO OPTIONS")]
 pub struct InfoOpts {
     /// Only print the number of records in the file
-    #[clap(short, long)]
+    #[clap(short, long, conflicts_with_all=["json", "show_index", "show_headers"])]
     pub num: bool,
 
+    /// Print the file in JSON format
+    #[clap(short, long, conflicts_with_all=["show_index", "show_headers", "num"])]
+    pub json: bool,
+
     /// Print the index of the file
-    #[clap(long)]
+    #[clap(long, conflicts_with_all=["json", "show_headers", "num"])]
     pub show_index: bool,
 
     /// Print the block headers of the file
-    #[clap(long, conflicts_with = "show_index")]
+    #[clap(long, conflicts_with_all=["json", "show_index", "num"])]
     pub show_headers: bool,
 }