Misc. changes

wang-q · Dec 2, 2024 · 77b23bc · 77b23bc
1 parent 586285d
commit 77b23bc
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 7 deletions.
diff --git a/templates/7_fill_anchors.tera.sh b/templates/7_fill_anchors.tera.sh
@@ -31,7 +31,7 @@ mkdir -p 7_fill_anchors
 
 log_info "overlap: between anchor-long"
 
-dazz overlap2 \
+anchr overlap2 \
     --parallel {{ opt.parallel }} \
     ${FILE_ANCHOR} \
     ${FILE_LONG} \
@@ -40,7 +40,7 @@ dazz overlap2 \
 
 cd 7_fill_anchors
 
-CONTIG_COUNT=$(faops n50 -H -N 0 -C anchor.fasta)
+CONTIG_COUNT=$(hnsm n50 -H -N 0 -C anchor.fasta)
 log_debug "contigs: ${CONTIG_COUNT}"
 
 log_info "group: anchor-long"
@@ -84,7 +84,7 @@ log_info "Build contigs"
 cat \
    group/non_grouped.fasta \
    group/*.contig.fasta |
-   faops filter -l 0 -a 1000 stdin contig.fasta
+   hnsm filter -a 1000 stdin -o contig.fasta
 
 log_info Done.
 

diff --git a/tests/cli_pl.rs b/tests/cli_pl.rs
@@ -78,16 +78,15 @@ fn command_overlap2() -> anyhow::Result<()> {
         eprintln!("bin = {:#?}", bin);
     }
 
-    let curdir = std::env::current_dir().unwrap();
-
     let tempdir = tempfile::TempDir::new().unwrap();
-    assert!(std::env::set_current_dir(&tempdir).is_ok());
 
     let mut cmd = Command::cargo_bin("anchr")?;
     let output = cmd
         .arg("overlap2")
         .arg("tests/ovlpr/1_4.anchor.fasta")
         .arg("tests/ovlpr/1_4.pac.fasta")
+        .arg("-d")
+        .arg(tempdir.path().display().to_string())
         .output()
         .unwrap();
     let stdout = String::from_utf8(output.stdout).unwrap();
@@ -97,7 +96,6 @@ fn command_overlap2() -> anyhow::Result<()> {
     assert!(&tempdir.path().join("anchorLong.db").is_file());
     assert!(&tempdir.path().join("anchorLong.ovlp.tsv").is_file());
 
-    assert!(std::env::set_current_dir(&curdir).is_ok());
     assert!(tempdir.close().is_ok());
 
     Ok(())