v0.1.4

CHANGELOG.md

@@ -1,4 +1,14 @@
-### v0.1.3 (pre)released - 2023-05-09 
+### v0.1.4 released - 2023-06-14
+
+#### Major
+* skani triangle had a bug where if more than 5000 queries were present and --sparse or -E was not specified, the intermediate batch of 5000 queries would be written in sparse mode. 
+* skani triangle -o was giving different upper triangle matrix instead of lower triangle (skani triangle > res gives lower triangle). Matrices are consistently lower triangle now.
+* Changed to lto = true for release mode. I see anywhere from a 5-10% speedup for this.
+
+#### Minor
+* Changed some dependencies so no more dependencies on old crates that will deprecate. 
+
+### v0.1.3 released - 2023-05-09 
 
 #### Major
 * Fixed a bug where memory was blowing up in `dist` and `triangle` when the marker-index was activated. For big datasets, there could be > 100 GBs of wasted memory. 

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "skani"
-version = "0.1.3"
+version = "0.1.4"
 edition = "2021"
 license = "MIT OR Apache-2.0"
 description = "skani is a fast tool for calculating ANI between metagenomic sequences, such as metagenome-assembled genomes (MAGs). It is extremely fast and is robust against incompleteness and fragmentation, giving accurate ANI estimates."

src/chain.rs

@@ -750,7 +750,7 @@ fn get_anchors(
     for anchor in anchors {
         if last_query_contig != anchor.query_contig || anchor.query_pos > curr_end_point {
             if query_positions_all[last_query_contig as usize].is_empty() {
-                warn!("{}", &query_sketch.contigs[(last_query_contig as usize)]);
+                warn!("{}", &query_sketch.contigs[last_query_contig as usize]);
                 continue;
             }
             let mut _num_seeds_in_block = 0;
@@ -800,7 +800,7 @@ fn get_anchors(
         let mut seed_pos_in_block = vec![];
         loop {
             if query_positions_all[last_query_contig as usize].is_empty() {
-                warn!("{}", &query_sketch.contigs[(last_query_contig as usize)]);
+                warn!("{}", &query_sketch.contigs[last_query_contig as usize]);
                 continue;
             }
             if running_counter >= query_positions_all[last_query_contig as usize].len() {

src/file_io.rs

@@ -414,7 +414,7 @@ pub fn write_phyllip_matrix(
             write!(&mut af_file, "{}", name).unwrap();
             let end = sketches.len();
             for j in 0..end {
-                let full_cond = (full_matrix && i >= j) || (i < j);
+                let full_cond = (full_matrix && i >= j) || (i > j);
                 if i == j {
                     if full_cond {
                         write!(&mut ani_file, "\t{:.2}", perfect).unwrap();

src/main.rs

@@ -21,7 +21,7 @@ static GLOBAL: tikv_jemallocator::Jemalloc = tikv_jemallocator::Jemalloc;
 fn main() {
     let matches = Command::new("skani")
         .setting(AppSettings::ArgRequiredElseHelp)
-        .version("0.1.3")
+        .version("0.1.4")
         .about("fast, robust ANI calculation and database searching for metagenomic contigs and assemblies. \n\nQuick ANI calculation:\nskani dist genome1.fa genome2.fa \n\nMemory-efficient database search:\nskani sketch genomes/* -o database; skani search -d database query1.fa query2.fa ...\n\nAll-to-all comparison:\nskani triangle genomes/*")
         .subcommand(
             SubCommand::with_name("help").setting(AppSettings::Hidden)
@@ -112,7 +112,7 @@ fn main() {
                 )
 
                 .help_heading("MISC")
-                .arg(Arg::new("v").short('v').help("Debug level verbosity."))
+                .arg(Arg::new("v").short('v').long("debug").help("Debug level verbosity."))
                 .arg(Arg::new("trace").long("trace").help("Trace level verbosity."))
 
             )
@@ -299,7 +299,7 @@ fn main() {
                         .help(H_NO_FULL_INDEX),
                 )
                 .help_heading("MISC")
-                .arg(Arg::new("v").short('v').help("Debug level verbosity."))
+                .arg(Arg::new("v").short('v').long("debug").help("Debug level verbosity."))
                 .arg(Arg::new("trace").long("trace").help("Trace level verbosity."))
         )
         .subcommand(
@@ -451,7 +451,7 @@ fn main() {
                         .help("Estimate median identity instead of average (mean) identity."),
                 )
                 .help_heading("MISC")
-                .arg(Arg::new("v").short('v').help("Debug level verbosity."))
+                .arg(Arg::new("v").short('v').long("debug").help("Debug level verbosity."))
                 .arg(Arg::new("trace").long("trace").help("Trace level verbosity."))
         )
         .subcommand(
@@ -571,7 +571,7 @@ fn main() {
                         .help("Estimate median identity instead of average (mean) identity."),
                 )
                 .help_heading("MISC")
-                .arg(Arg::new("v").short('v').help("Debug level verbosity."))
+                .arg(Arg::new("v").short('v').long("debug").help("Debug level verbosity."))
                 .arg(Arg::new("trace").long("trace").help("Trace level verbosity."))
 
         )

src/triangle.rs

@@ -103,7 +103,7 @@ pub fn triangle(command_params: CommandParams, mut sketch_params: SketchParams)
             }
             if c % 100 == 0 && c != 0 {
                 info!("{} query sequences processed.", c);
-                if c % INTERMEDIATE_WRITE_COUNT == 0 && c != 0 {
+                if c % INTERMEDIATE_WRITE_COUNT == 0 && c != 0 && command_params.sparse{
                     let moved_anis: FxHashMap<_,_>;
                     {
                         let mut locked = anis.lock().unwrap();