Kvg multiple windows (#33)

* Find superbubbles in graph
* When a superbubble has more than two paths, trim off the low quality ones

src/hidive/src/correct.rs

@@ -12,32 +12,29 @@ pub fn start(
     gfa_output: Option<PathBuf>,
     kmer_size: usize,
     model_path: &PathBuf,
-    long_read_fasta_paths: &Vec<PathBuf>,
-    short_read_fasta_paths: &Vec<PathBuf>,
+    long_read_fasta_path: &PathBuf,
+    short_read_fasta_path: &PathBuf,
 ) {
-    let long_read_seq_urls = skydive::parse::parse_file_names(long_read_fasta_paths);
-    let short_read_seq_urls = skydive::parse::parse_file_names(short_read_fasta_paths);
+    let long_read_seq_urls = skydive::parse::parse_file_names(&[long_read_fasta_path.clone()]);
+    let short_read_seq_urls = skydive::parse::parse_file_names(&[short_read_fasta_path.clone()]);
 
     // Read all long reads.
     skydive::elog!("Processing long-read samples {:?}...", long_read_seq_urls.iter().map(|url| url.as_str()).collect::<Vec<&str>>());
-    let all_lr_seqs = skydive::utils::read_fasta(long_read_fasta_paths);
+    let all_lr_seqs = skydive::utils::read_fasta(&vec![long_read_fasta_path.clone()]);
 
     // Read all short reads.
     skydive::elog!("Processing short-read samples {:?}...", short_read_seq_urls.iter().map(|url| url.as_str()).collect::<Vec<&str>>());
-    let all_sr_seqs = skydive::utils::read_fasta(short_read_fasta_paths);
+    let all_sr_seqs = skydive::utils::read_fasta(&vec![short_read_fasta_path.clone()]);
 
     let l1 = LdBG::from_sequences("lr".to_string(), kmer_size, &all_lr_seqs);
     let s1 = LdBG::from_sequences("sr".to_string(), kmer_size, &all_sr_seqs);
 
     let m = MLdBG::from_ldbgs(vec![l1, s1])
         .score_kmers(model_path)
         .collapse()
-        .clean_color_specific_paths(1, 0.2)
-        .clean_tangles(1, 100, 0.2)
-        .clean_branches(0.01)
-        .clean_tips(3*kmer_size, 0.01)
-        .clean_contigs(100)
-        .build_links(&all_lr_seqs, false);
+        .clean(0.2, 0.01)
+        .build_links(&all_lr_seqs, true)
+        ;
 
     skydive::elog!("Built MLdBG with {} k-mers.", m.kmers.len());
 
@@ -52,8 +49,7 @@ pub fn start(
 
     let progress_bar = skydive::utils::default_bounded_progress_bar("Correcting reads", all_lr_seqs.len() as u64);
 
-    let corrected_seqs =
-        all_lr_seqs
+    let corrected_seqs = all_lr_seqs
         .par_iter()
         .progress_with(progress_bar)
         .map(|seq| m.correct_seq(seq))

src/hidive/src/main.rs

@@ -288,13 +288,13 @@ enum Commands {
         #[clap(short, long, required = true, value_parser)]
         model_path: PathBuf,
 
-        /// FASTA files with short-read sequences (may contain one or more samples).
-        #[clap(short, long, required = false, value_parser)]
-        short_read_fasta_paths: Vec<PathBuf>,
-
         /// FASTA files with long-read sequences (may contain one or more samples).
         #[clap(required = true, value_parser)]
-        long_read_fasta_paths: Vec<PathBuf>,
+        long_read_fasta_path: PathBuf,
+
+        /// FASTA files with short-read sequences (may contain one or more samples).
+        #[clap(required = true, value_parser)]
+        short_read_fasta_path: PathBuf,
     },
 
     /// Co-assemble target locus from long- and short-read data using a linked de Bruijn graph.
@@ -421,10 +421,10 @@ fn main() {
             gfa_output,
             kmer_size,
             model_path,
-            long_read_fasta_paths,
-            short_read_fasta_paths,
+            long_read_fasta_path,
+            short_read_fasta_path,
         } => {
-            correct::start(&output, gfa_output, kmer_size, &model_path, &long_read_fasta_paths, &short_read_fasta_paths);
+            correct::start(&output, gfa_output, kmer_size, &model_path, &long_read_fasta_path, &short_read_fasta_path);
         }
         Commands::Coassemble {
             output,

src/skydive/Cargo.toml

@@ -35,6 +35,7 @@ openssl = { version = "0.10", features = ["vendored"] }
 path-absolutize = "3.1.1"
 parquet = "52.1.0"
 petgraph = "0.6.5"
+poasta = { git = "https://github.com/broadinstitute/poasta.git" }
 #polars = { version = "*", features = ["parquet", "lazy", "csv-file", "strings", "temporal", "dtype-duration", "dtype-categorical", "concat_str", "list", "list_eval", "rank", "lazy_regex"]}
 pyo3 = { version = "0.20.0", features = ["abi3-py37", "extension-module"] }
 pyo3-asyncio = { version = "0.20.0", features = ["attributes", "async-std-runtime", "tokio-runtime"] }