fix: fix bug during calculation of read position bias (#422)

### Description

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### QC
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* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation at
https://github.com/varlociraptor/varlociraptor.github.io is updated in a
separate PR to reflect the changes or this is not necessary (e.g. if the
change does neither modify the calling grammar nor the behavior or
functionalities of Varlociraptor).

src/variants/evidence/observations/read_observation.rs

@@ -516,18 +516,30 @@ where
 pub(crate) fn major_read_position(
     pileup: &[ReadObservation<Option<u32>, ExactAltLoci>],
 ) -> Option<u32> {
-    calc_major_feature(pileup.iter().filter_map(|obs| obs.read_position))
+    calc_major_feature(pileup.iter().filter_map(|obs| {
+        if obs.prob_alt > obs.prob_ref {
+            obs.read_position
+        } else {
+            None
+        }
+    }))
 }
 
 pub(crate) fn major_alt_locus(
     pileup: &[ReadObservation<Option<u32>, ExactAltLoci>],
     alignment_properties: &AlignmentProperties,
 ) -> Option<genome::Locus> {
-    calc_major_feature(pileup.iter().flat_map(|obs| {
-        obs.alt_locus
+    calc_major_feature(
+        pileup
             .iter()
-            .map(|locus| locus_to_bucket(locus, alignment_properties))
-    }))
+            // TODO filter for alt obs only?
+            //.filter(|obs| obs.prob_alt > obs.prob_ref)
+            .flat_map(|obs| {
+                obs.alt_locus
+                    .iter()
+                    .map(|locus| locus_to_bucket(locus, alignment_properties))
+            }),
+    )
 }
 
 pub(crate) fn locus_to_bucket(

src/variants/model/bias/alt_locus_bias.rs

@@ -36,7 +36,7 @@ impl Bias for AltLocusBias {
     fn prob_ref(&self, observation: &ProcessedReadObservation) -> LogProb {
         // METHOD: ref reads should not point to the alt locus. The reason is that in that case,
         // the homology does not appear to be variant specific, and hence the normal MAPQs
-        // should be able to capure it.
+        // should be able to capture it.
         match (self, observation.is_max_mapq, observation.alt_locus) {
             (AltLocusBias::None, _, _) => *PROB_05, // normal
             (AltLocusBias::Some, true, AltLocus::Some | AltLocus::None) => LogProb::ln_one(), // no bias