Merge pull request #21 from esteinig/test_ci

test ci/cd

src/align.rs

@@ -822,12 +822,14 @@ impl ReadAlignment {
         Ok(())
     }
 
+    #[allow(clippy::too_many_arguments)]
     pub fn group_output(
         &self,
         coverage_fields: &[CoverageFields],
         grouped_regions: u64,
         grouped_coverage: f64,
         grouped_alignments: u64,
+        grouped_reads: u64,
         group_by: String,
         group_sep: String,
     ) -> Result<Vec<CoverageFields>, ReadAlignmentError> {
@@ -915,6 +917,7 @@ impl ReadAlignment {
             if grouped_fields.regions >= grouped_regions
                 && grouped_fields.coverage >= grouped_coverage
                 && grouped_fields.alignments >= grouped_alignments
+                && grouped_fields.reads >= grouped_reads
             {
                 grouped_coverage_fields.push(grouped_fields);
             }

src/cli.rs

@@ -8,15 +8,14 @@ use structopt::StructOpt;
 pub struct Cli {
     /// Alignment file (SAM/BAM/CRAM/PAF)
     #[structopt(
-        short, long, parse(try_from_os_str = check_file_exists), required = true
+        short = "i", long, parse(try_from_os_str = check_file_exists), required = true
     )]
     pub alignment: PathBuf,
     /// bam: SAM/BAM/CRAM alignment; paf: PAF alignment
     ///
     /// Default is to attempt to infer the input alignment format automatically from the filename
     /// extension (bam|sam|cram|paf). This option is used to override that.
     #[structopt(
-        short = "i",
         long,
         value_name = "bam|paf",
         possible_values = &["bam", "paf"],
@@ -92,15 +91,15 @@ pub struct Cli {
     ///   - unique reads are recomputed across members of the group
     ///   - covered base pairs in the reference sequence lengths are set to 0
     ///   - coverage is selected to be the highest by a member of the group.
-    #[structopt(short, long)]
+    #[structopt(short = "g", long)]
     pub group_by: Option<String>,
     /// Group field separator in the reference sequence description
     ///
     /// Often there are multiple fields in the header of the reference
     /// sequences (e.g. taxid=1101 | taxname=argh). A delimitor needs to
     /// be specified to signal the end of a specific grouping field
     /// (e.g. --group-sep "|" with --group-by "taxid=").
-    #[structopt(long, default_value = ";")]
+    #[structopt(short = "s", long, default_value = ";")]
     pub group_sep: String,
     /// A file with a string per line to exclude alignments
     /// if the string occurs in the target sequence description
@@ -193,6 +192,12 @@ pub struct Cli {
     /// across reference sequences if results are grouped
     #[structopt(long, default_value = "0")]
     pub group_aligned: u64,
+    /// Minimum grouped coverage reads
+    ///
+    /// Filters results by a minimum number of unique reads
+    /// across reference sequences if results are grouped
+    #[structopt(long, default_value = "0")]
+    pub group_reads: u64,
     /// Output read identifiers of all alignments to file
     ///
     /// Creates a file (.txt) that contains the identifiers

src/main.rs

@@ -75,6 +75,7 @@ fn main() -> Result<(), ReadAlignmentError> {
                                 args.group_regions,
                                 args.group_coverage,
                                 args.group_aligned,
+                                args.group_reads,
                                 group_field,
                                 args.group_sep.clone(),
                             )?;