polbin: Finish loading binary files (#151)

polbin/Cargo.toml

@@ -6,5 +6,6 @@ edition = "2021"
 [dependencies]
 bstr = "1.9.1"
 gfa = "0.10.1"
+memmap = "0.7.0"
 num_enum = "0.7.2"
 zerocopy = { version = "0.7.32", features = ["derive"] }

polbin/src/file.rs

@@ -1,5 +1,4 @@
 use crate::flatgfa;
-use bstr::BStr;
 use zerocopy::{FromBytes, FromZeroes};
 
 const MAGIC_NUMBER: usize = 0x1337_4915;
@@ -14,36 +13,48 @@ struct TOC {
     steps_count: usize,
     seq_data_len: usize,
     overlaps_count: usize,
-    alignment_len: usize,
+    alignment_count: usize,
     name_data_len: usize,
     optional_data_len: usize,
     line_order_len: usize,
 }
 
-pub fn load(data: &[u8]) -> flatgfa::FlatGFA {
+/// Get the first `len` bytes in a byte slice, and return the rest of the slice.
+fn get_prefix(data: &[u8], len: usize) -> (&[u8], &[u8]) {
+    assert!(data.len() >= len);
+    (&data[0..len], &data[len..])
+}
+
+pub fn view(data: &[u8]) -> flatgfa::FlatGFA {
     // Table of contents.
     let toc = TOC::ref_from_prefix(data).unwrap();
     let rest = &data[std::mem::size_of::<TOC>()..];
     assert_eq!(toc.magic, MAGIC_NUMBER);
 
-    // Header (version).
-    let header = BStr::new(&rest[0..toc.header_len]);
-    let rest = &rest[toc.header_len..];
-
-    // Segments.
+    // Get slices for each chunk.
+    let (header, rest) = get_prefix(rest, toc.header_len);
     let (segs, rest) = flatgfa::Segment::slice_from_prefix(rest, toc.segs_count).unwrap();
+    let (paths, rest) = flatgfa::Path::slice_from_prefix(rest, toc.paths_count).unwrap();
+    let (links, rest) = flatgfa::Link::slice_from_prefix(rest, toc.links_count).unwrap();
+    let (steps, rest) = flatgfa::Handle::slice_from_prefix(rest, toc.steps_count).unwrap();
+    let (seq_data, rest) = get_prefix(rest, toc.seq_data_len);
+    let (overlaps, rest) = flatgfa::Span::slice_from_prefix(rest, toc.overlaps_count).unwrap();
+    let (alignment, rest) = flatgfa::AlignOp::slice_from_prefix(rest, toc.alignment_count).unwrap();
+    let (name_data, rest) = get_prefix(rest, toc.name_data_len);
+    let (optional_data, rest) = get_prefix(rest, toc.optional_data_len);
+    let (line_order, _) = get_prefix(rest, toc.line_order_len);
 
     flatgfa::FlatGFA {
-        header,
+        header: header.into(),
         segs,
-        paths: todo!(),
-        links: todo!(),
-        steps: todo!(),
-        seq_data: todo!(),
-        overlaps: todo!(),
-        alignment: todo!(),
-        name_data: todo!(),
-        optional_data: todo!(),
-        line_order: todo!(),
+        paths,
+        links,
+        steps,
+        seq_data,
+        overlaps,
+        alignment,
+        name_data: name_data.into(),
+        optional_data: optional_data.into(),
+        line_order,
     }
 }

polbin/src/main.rs

@@ -2,10 +2,23 @@ mod file;
 mod flatgfa;
 mod parse;
 mod print;
+use memmap::Mmap;
+
+fn map_file(name: &str) -> Mmap {
+    let file = std::fs::File::open(name).unwrap();
+    unsafe { Mmap::map(&file) }.unwrap()
+}
 
 fn main() {
-    let stdin = std::io::stdin();
-    let store = parse::Parser::parse(stdin.lock());
-    let gfa = store.view();
-    print::print(&gfa);
+    // Read either GFA text from stdin or a binary file from the first argument.
+    if let Some(name) = std::env::args().nth(1) {
+        let mmap = map_file(&name);
+        let gfa = file::view(&mmap);
+        print::print(&gfa);
+    } else {
+        let stdin = std::io::stdin();
+        let store = parse::Parser::parse(stdin.lock());
+        let gfa = store.view();
+        print::print(&gfa);
+    }
 }