Clean up some of the filter logging messages

src/generic_modes.rs

@@ -241,7 +241,7 @@ pub fn weed<IntT: for<'a> UInt<'a>>(
     }
 
     let filter_threshold = f64::floor(ska_array.nsamples() as f64 * min_freq) as usize;
-    if filter_threshold > 0 || *filter != FilterType::NoFilter || ambig_mask {
+    if filter_threshold > 0 || *filter != FilterType::NoFilter || ambig_mask || ignore_const_gaps {
         log::info!("Applying filters: threshold={filter_threshold} constant_site_filter={filter} ambig_mask={ambig_mask} no_gap_only_sites={ignore_const_gaps}");
         let update_kmers = true;
         ska_array.filter(

src/merge_ska_array.rs

@@ -154,7 +154,6 @@ where
 
     /// Load a split k-mer array from a `.skf` file.
     pub fn load(filename: &str) -> Result<Self, Box<dyn Error>> {
-        log::info!("Loading skf file");
         let ska_file = BufReader::new(File::open(filename)?);
         let decompress_reader = snap::read::FrameDecoder::new(ska_file);
         let ska_obj: Self = ciborium::de::from_reader(decompress_reader)?;
@@ -251,6 +250,10 @@ where
         ignore_const_gaps: bool,
         update_kmers: bool,
     ) -> i32 {
+        if ignore_const_gaps && matches!(filter, FilterType::NoAmbig | FilterType::NoFilter) {
+            log::warn!("--no-gap-only-sites can only be applied when filtering constant bases")
+        }
+
         let total = self.names.len();
         let mut filtered_variants = Array2::zeros((0, total));
         let mut filtered_counts = Vec::new();

tests/align.rs

@@ -165,6 +165,7 @@ fn filters() {
         .arg(sandbox.file_string("merge_k9.skf", TestDir::Input))
         .arg("--filter")
         .arg("no-filter")
+        .arg("--no-gap-only-sites") // adding with no filter produces a warning
         .arg("-v")
         .output()
         .unwrap()