fixed app tests

esteinig · Feb 18, 2023 · 3dfe52f · 3dfe52f
1 parent 69898fa
commit 3dfe52f
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Showing 2 changed files with 18 additions and 41 deletions.
diff --git a/src/cli.rs b/src/cli.rs
@@ -114,7 +114,7 @@ pub struct Cli {
     /// Output the coverage statistics as a pretty table; may still get
     /// mangled on short terminals, as terminal width cannot currently
     /// be estimated in underlying library.
-    #[structopt(short = "t", long = "table")]
+    #[structopt(short = "T", long = "table")]
     pub table: bool,
     /// Prints coverage plots
     ///
@@ -149,7 +149,7 @@ pub struct Cli {
     /// with fewer distinct alignment regions to pass the basic filter. For example,
     /// a reference sequence with 100% coverage and 1 distinct alignment regions would
     /// not be filtered from the report output.
-    #[structopt(short = "r", long = "regions-coverage")]
+    #[structopt(short = "t", long = "regions-coverage")]
     pub regions_coverage: Option<f64>,
     /// Minimum read threshold (unique reads in alignment)
     ///

diff --git a/tests/app.rs b/tests/app.rs
@@ -5,7 +5,7 @@ use std::process::Command;
 #[test]
 fn input_file_doesnt_exist() -> Result<(), Box<dyn std::error::Error>> {
     let mut cmd = Command::cargo_bin(env!("CARGO_PKG_NAME"))?;
-    cmd.args(vec!["--paf", "file/doesnt/exist.paf"]);
+    cmd.args(vec!["--alignment", "file/doesnt/exist.paf"]);
     cmd.assert()
         .failure()
         .stderr(predicate::str::contains("does not exist"));
@@ -17,7 +17,7 @@ fn input_file_doesnt_exist() -> Result<(), Box<dyn std::error::Error>> {
 fn valid_inputs_raise_no_errors() -> Result<(), Box<dyn std::error::Error>> {
     let mut cmd = Command::cargo_bin(env!("CARGO_PKG_NAME"))?;
     cmd.args(vec![
-        "--paf",
+        "--alignment",
         "tests/cases/test_ok.paf",
         "--fasta",
         "tests/cases/test_paf_ok.fasta",
@@ -33,37 +33,14 @@ fn valid_inputs_raise_no_errors() -> Result<(), Box<dyn std::error::Error>> {
 fn valid_output_string_default_filters() -> Result<(), Box<dyn std::error::Error>> {
     let mut cmd = Command::cargo_bin(env!("CARGO_PKG_NAME"))?;
     cmd.args(vec![
-        "--paf",
+        "--alignment",
         "tests/cases/test_ok.paf",
         "--fasta",
         "tests/cases/test_paf_ok.fasta",
     ]);
 
     cmd.assert().success().stdout(predicate::str::contains(
-        "21172389_LCMV_L-segment_final\t2\t1\t2\t273\t7194\t0.0379\t",
-    ));
-
-    Ok(())
-}
-
-#[test]
-fn valid_output_string_no_filters() -> Result<(), Box<dyn std::error::Error>> {
-    let mut cmd = Command::cargo_bin(env!("CARGO_PKG_NAME"))?;
-    cmd.args(vec![
-        "--paf",
-        "tests/cases/test_ok.paf",
-        "--fasta",
-        "tests/cases/test_paf_ok.fasta",
-        "--min-mapq",
-        "0",
-        "--min-len",
-        "0",
-        "--min-cov",
-        "0",
-    ]);
-
-    cmd.assert().success().stdout(predicate::str::contains(
-        "21172389_LCMV_L-segment_final\t3\t2\t3\t321\t7194\t0.0446\t-\t-\n21172389_LCMV_S-segment_final\t2\t2\t2\t137\t3407\t0.0402\t-\t-"
+        "21172389_LCMV_L-segment_final\t3\t2\t3\t321\t7194\t0.0446\t-\t-\n21172389_LCMV_S-segment_final\t2\t2\t2\t137\t3407\t0.0402\t-\t-\n"
     ));
 
     Ok(())
@@ -74,15 +51,15 @@ fn valid_output_string_default_filters_verbose_one_no_descr(
 ) -> Result<(), Box<dyn std::error::Error>> {
     let mut cmd = Command::cargo_bin(env!("CARGO_PKG_NAME"))?;
     cmd.args(vec![
-        "--paf",
+        "--alignment",
         "tests/cases/test_ok.paf",
         "--fasta",
         "tests/cases/test_paf_ok.fasta",
         "-v",
     ]);
 
     cmd.assert().success().stdout(predicate::str::contains(
-        "21172389_LCMV_L-segment_final\t2\t1\t2\t273\t7194\t0.0379\t-\t-",
+        "21172389_LCMV_L-segment_final\t3\t2\t3\t321\t7194\t0.0446\t-\t-",
     ));
 
     Ok(())
@@ -93,16 +70,16 @@ fn valid_output_string_default_filters_region_threshold_pass(
 ) -> Result<(), Box<dyn std::error::Error>> {
     let mut cmd = Command::cargo_bin(env!("CARGO_PKG_NAME"))?;
     cmd.args(vec![
-        "--paf",
+        "--alignment",
         "tests/cases/test_ok.paf",
         "--fasta",
         "tests/cases/test_paf_ok.fasta",
-        "-r",
+        "--regions",
         "2",
     ]);
 
     cmd.assert().success().stdout(predicate::str::contains(
-        "21172389_LCMV_L-segment_final\t2\t1\t2\t273\t7194\t0.0379\t",
+        "21172389_LCMV_L-segment_final\t3\t2\t3\t321\t7194\t0.0446\t-\t-",
     ));
 
     Ok(())
@@ -113,11 +90,11 @@ fn valid_output_string_default_filters_region_threshold_none(
 ) -> Result<(), Box<dyn std::error::Error>> {
     let mut cmd = Command::cargo_bin(env!("CARGO_PKG_NAME"))?;
     cmd.args(vec![
-        "--paf",
+        "--alignment",
         "tests/cases/test_ok.paf",
         "--fasta",
         "tests/cases/test_paf_ok.fasta",
-        "-r",
+        "--regions",
         "3",
     ]);
 
@@ -131,16 +108,16 @@ fn valid_output_string_default_filters_refseq_length_pass() -> Result<(), Box<dy
 {
     let mut cmd = Command::cargo_bin(env!("CARGO_PKG_NAME"))?;
     cmd.args(vec![
-        "--paf",
+        "--alignment",
         "tests/cases/test_ok.paf",
         "--fasta",
         "tests/cases/test_paf_ok.fasta",
-        "-s",
+        "--length",
         "5000",
     ]);
 
     cmd.assert().success().stdout(predicate::str::contains(
-        "21172389_LCMV_L-segment_final\t2\t1\t2\t273\t7194\t0.0379\t",
+        "21172389_LCMV_L-segment_final\t3\t2\t3\t321\t7194\t0.0446\t-\t-",
     ));
 
     Ok(())
@@ -151,11 +128,11 @@ fn valid_output_string_default_filters_refseq_length_none() -> Result<(), Box<dy
 {
     let mut cmd = Command::cargo_bin(env!("CARGO_PKG_NAME"))?;
     cmd.args(vec![
-        "--paf",
+        "--alignment",
         "tests/cases/test_ok.paf",
         "--fasta",
         "tests/cases/test_paf_ok.fasta",
-        "-s",
+        "--length",
         "8000",
     ]);