Fix tests, change command line call parameters

DavidsonGroup · Jan 2, 2025 · 89c306f · 89c306f
1 parent 05c4054
commit 89c306f
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Showing 5 changed files with 18 additions and 22 deletions.
diff --git a/src/cli.rs b/src/cli.rs
@@ -42,8 +42,8 @@ pub enum Commands {
         preset: crate::preset::PresetBarcodeFormats,
 
         /// the output index file
-        #[arg(long, default_value = "index.tsv")]
-        index: String,
+        #[arg(short, default_value = "index.tsv")]
+        output: String,
 
         /// whether to use a file containing pre-clustered reads, with every line in one of two formats:
         ///   1. READ_ID;BARCODE
@@ -94,7 +94,7 @@ pub enum Commands {
         index: String,
 
         /// output file
-        #[arg(long, default_value = "summary.html")]
+        #[arg(short, default_value = "summary.html")]
         output: String,
     },
 
@@ -109,8 +109,8 @@ pub enum Commands {
         #[arg(long)]
         input: String,
 
-        /// the output .fasta; note that quality values are not preserved
-        #[arg(long)]
+        /// the output .fastq
+        #[arg(short)]
         output: Option<String>,
 
         /// the number of threads to use
@@ -137,7 +137,7 @@ pub enum Commands {
         #[arg(long)]
         input: String,
 
-        #[arg(long)]
+        #[arg(short)]
         output: Option<String>,
     },
 }

diff --git a/src/main.rs b/src/main.rs
@@ -66,7 +66,7 @@ fn try_main() -> Result<()> {
         }
         Commands::Index {
             file,
-            index,
+            output,
             preset,
             barcode_regex,
             clusters,
@@ -93,13 +93,14 @@ fn try_main() -> Result<()> {
 
             index::construct_index(
                 file,
-                index,
+                output,
                 &barcode_regex,
                 *skip_unmatched,
                 clusters,
                 filter_opts,
             )?;
-            info!("Completed index generation to {index}");
+
+            info!("Completed index generation to {output}");
         }
         Commands::Call {
             index,

diff --git a/tests/correct/consensus.fastq b/tests/correct/consensus.fastq
diff --git a/tests/correct/index.tsv b/tests/correct/index.tsv
@@ -1,4 +1,4 @@
-#{"nailpolish_version":"0.1.0","file_path":"/Users/olliecheng/Developer/WEHI/consensus-call/nailpolish/tests/data/scmixology2_sample.fastq","index_date":"2025-01-02T10:46:32.316021+08:00","elapsed":0.526168292,"gb":0.02817634679377079,"matched_read_count":14142,"unmatched_read_count":0,"read_count":14143,"avg_qual":21274.992292462168,"avg_len":1009.505232640362,"filtered_reads":1}
+#{"nailpolish_version":"0.1.0","file_path":"/Users/olliecheng/Developer/WEHI/consensus-call/nailpolish/tests/data/scmixology2_sample.fastq","index_date":"2025-01-02T10:50:28.741895+08:00","elapsed":0.023255041,"gb":0.02817634679377079,"matched_read_count":14142,"unmatched_read_count":0,"read_count":14143,"avg_qual":21274.992292462168,"avg_len":1009.505232640362,"filtered_reads":1}
 id	pos	avg_qual	n_bases	rec_len
 TCTGGCTCATTCTCCG_GCAGCGAAGCCC	0	19.47	593	1264
 GCACTAAGTTGAAGTA_ATCAATGTATTG	1264	9.52	1655	3388

diff --git a/tests/integration_test.rs b/tests/integration_test.rs
@@ -11,12 +11,7 @@ fn index() {
     let mut command = Command::cargo_bin("nailpolish").unwrap();
 
     let _ = command
-        .args(&[
-            "index",
-            SAMPLE_FASTQ,
-            "--index",
-            temp.path().to_str().unwrap(),
-        ])
+        .args(&["index", SAMPLE_FASTQ, "-o", temp.path().to_str().unwrap()])
         .assert()
         .success();
 
@@ -43,7 +38,7 @@ fn summary() {
             "summary",
             "--index",
             "tests/correct/index.tsv",
-            "--output",
+            "-o",
             temp.path().to_str().unwrap(),
         ])
         .assert()
@@ -65,7 +60,7 @@ fn consensus_1t() {
             "tests/correct/index.tsv",
             "--input",
             SAMPLE_FASTQ,
-            "--output",
+            "-o",
             temp.path().to_str().unwrap(),
             "--threads",
             "1",
@@ -94,7 +89,7 @@ fn consensus_4t() {
             "tests/correct/index.tsv",
             "--input",
             SAMPLE_FASTQ,
-            "--output",
+            "-o",
             temp.path().to_str().unwrap(),
             "--threads",
             "4",