Add CLI entry point for pangenotype matrix

Author: sampsyo

flatgfa/src/cli/cmds.rs

@@ -338,3 +338,26 @@ pub fn bed_intersect(args: BEDIntersect) {
         }
     }
 }
+
+/// construct a pangenotype matrix
+#[derive(FromArgs, PartialEq, Debug)]
+#[argh(subcommand, name = "matrix")]
+pub struct PangenotypeMatrix {
+    /// the GAF file to use for genotyping
+    #[argh(positional)]
+    gaf_file: String,
+}
+
+pub fn pangenotype_matrix(gfa: &flatgfa::FlatGFA, args: PangenotypeMatrix) {
+    let matrix = ops::pangenotype::make_pangenotype_matrix(gfa, vec![args.gaf_file]);
+    for row in matrix {
+        for col in row {
+            if col {
+                print!("1");
+            } else {
+                print!("0");
+            }
+        }
+        println!();
+    }
+}

flatgfa/src/cli/main.rs

@@ -44,6 +44,7 @@ enum Command {
     GafLookup(cmds::GAFLookup),
     Bench(cmds::Bench),
     BedIntersect(cmds::BEDIntersect),
+    PangenotypeMatrix(cmds::PangenotypeMatrix),
 }
 
 fn main() -> Result<(), &'static str> {
@@ -146,6 +147,9 @@ fn main() -> Result<(), &'static str> {
         Some(Command::BedIntersect(_sub_args)) => {
             panic!("Unreachable code");
         }
+        Some(Command::PangenotypeMatrix(sub_args)) => {
+            cmds::pangenotype_matrix(&gfa, sub_args);
+        }
         None => {
             // Just emit the GFA or FlatGFA file.
             dump(&gfa, &args.output);