logging in pair overlap

fulcrumgenomics · Aug 24, 2023 · 7a2e646 · 7a2e646
1 parent 6201ea1
commit 7a2e646
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Showing 3 changed files with 27 additions and 4 deletions.
diff --git a/src/bin/commands/trimmer.rs b/src/bin/commands/trimmer.rs
@@ -56,7 +56,7 @@ pub(crate) struct TrimmerOpts {
     #[clap(long, default_value = "15")]
     osc_window: usize,
 
-    /// Required of oscillations in a window to trigger trimming/masking.
+    /// Required number of oscillations in a window to trigger trimming/masking.
     #[clap(long, default_value = "4")]
     osc_max_oscillations: usize,
 
@@ -173,6 +173,13 @@ impl Command for TrimmerOpts {
                             self.overlap_min_length,
                             self.overlap_max_error_rate,
                         ) {
+                            log::debug!(
+                                "found overlap in pair: {} shift: {}, overlap: {}, adapter: {}",
+                                r1.id().unwrap_or("read"),
+                                overlap.shift,
+                                overlap.overlap,
+                                overlap.adapter
+                            );
                             stats.overlap_stats.update(overlap);
                             let corrections = overlap.correct(
                                 &mut r1,
@@ -184,6 +191,7 @@ impl Command for TrimmerOpts {
                                     Some(self.mask_quality)
                                 },
                             );
+                            log::debug!("corrections: {:?}", corrections);
                             stats.overlap_stats.update_corrections(corrections.0, stats::ReadI::R1);
                             stats.overlap_stats.update_corrections(corrections.1, stats::ReadI::R2);
                         }

diff --git a/src/lib/base_quality.rs b/src/lib/base_quality.rs
@@ -31,11 +31,12 @@ pub fn identify_trim_point(
     // here we have indices of oscillations. e.g.: [50, 52, 53, 54, 55, 57, 58, 59, 60, 62, 63, 64, 65, 67, 68, 69, 70, 72, 73, 74]
 
     // use a window of `max_oscilations` and check if there are at least `max_oscillations` oscillations in the window.
-    osc.windows(max_oscillations).find(|w| 
+    osc.windows(max_oscillations)
+        .find(|w|
         // given a e.g. [50, 52, 55] means we found 3 oscillations in 5 bases (55 - 50)
         // and we had window_size to find that many. so if the last - first < window_size, we found an osc window.
-        w[w.len() - 1] - w[0] < window_size
-    ).map(|w| w[0])
+        w[w.len() - 1] - w[0] < window_size)
+        .map(|w| w[0])
 }
 
 // Indicates which tail(s) to clip.

diff --git a/src/lib/pair_overlap.rs b/src/lib/pair_overlap.rs
@@ -68,10 +68,24 @@ impl PairOverlap {
             } else {
                 // when bases disagree, set the lower quality base to the higher quality base.
                 if r1_quals[i + self.shift] >= r2_quals[i] + bq_delta {
+                    log::debug!(
+                        "correcting read2 at {} with read1 at {}, base: {} to {}",
+                        i,
+                        i + self.shift,
+                        r2_seq[i] as char,
+                        r1_seq[i + self.shift] as char
+                    );
                     r2_seq[i] = r1_seq[i + self.shift];
                     r2_quals[i] = r1_quals[i + self.shift];
                     correction_counts.1 += 1;
                 } else if r2_quals[i] >= r1_quals[i + self.shift] + bq_delta {
+                    log::debug!(
+                        "correcting read1 at {} with read2 at {}, base: {} to {}",
+                        i + self.shift,
+                        i,
+                        r1_seq[i + self.shift] as char,
+                        r2_seq[i] as char
+                    );
                     r1_seq[i + self.shift] = r2_seq[i];
                     r1_quals[i + self.shift] = r2_quals[i];
                     correction_counts.0 += 1;