Include short preface in README

README.md

@@ -4,6 +4,22 @@ Perform hard selective masking of ancient DNA deamination patterns, using the ou
 
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+# Preface
+
+`pmd-mask` is a simple preprocessing and quality filtration command-line utility designed to selectively mask potentially deaminated nucleotides within ancient DNA alignement files, changing putative deaminated bases to ‘N’ and quality to ‘!’.
+
+This method may be regarded as a conservative compromise between post-morterm damage rescaling methods such as [MapDamage](https://ginolhac.github.io/mapDamage/) or [PMDtools](https://github.com/pontussk/PMDtools), and hard-clipping methods such as [`bamUtils trimBam`]. Here, `pmd-mask` instead leverages nucleotide and position specific misincorporation rate estimes emitted from [MapDamage](https://ginolhac.github.io/mapDamage/) to selectively trim read ends, up-until the local misincorporation rate reaches a designated, user-defined threshold (default: 1%). This approach can thus greatly mitigate the loss of information usually displayed when applying hard-clipping on ancient DNA samples, by *specifically* targeting potential `C>T` and `G>A` transitions on both the 5’ and 3’ end of the read, respectively.
+
+
+<p align="center">
+  <figure align="center">
+    <img src="docs/images/preface-illustration.png" alt="An illustration of how pmd-mask operates" title="This is a Title"> 
+    <figcaption>
+      <em>Figure 1.</em> An illustration of how pmd-mask operates. 
+    </figcaption>
+  </figure>
+</p>
+
 
 # Installation
 

src/genome/coordinate/position.rs

@@ -1,4 +1,4 @@
-use std::{fmt::{self, Display, Formatter}};
+use std::fmt::{self, Display, Formatter};
 use serde::Deserialize;
 
 /// Absolute or relative position within a chromosome or read (in base pairs).

src/genome/orientation/mod.rs

@@ -1,4 +1,4 @@
-use std::{fmt::{self, Display, Formatter}};
+use std::fmt::{self, Display, Formatter};
 use serde::Deserialize;
 
 /// Encodes the orientation of a relative bam record position. Two possible variants:  

src/genome/strand/mod.rs

@@ -168,4 +168,9 @@ mod test {
         assert_eq!(Strand::from_str("*"), Err(StrandError::ParseStrand("*".to_string())));
     }
 
+    #[test]
+    fn from_char() {
+        assert_eq!('+', std::convert::Into::<char>::into(Strand::Forward));
+        assert_eq!('-', std::convert::Into::<char>::into(Strand::Reverse));
+    }
 }

src/mask/mod.rs

@@ -59,7 +59,7 @@ impl TryFrom<&Misincorporations> for Masks {
         for position in value.iter() {
             let record = MaskEntry{chromosome: position.chromosome.clone(), strand: position.strand};
             masks.inner.entry(record)
-                .or_insert(MaskThreshold::default())
+                .or_default()
                 .set_threshold(position.end, position.position);
         }
 
@@ -229,7 +229,7 @@ mod test {
             mis_record!("chr1", Reverse, FivePrime,  8, 1000, 0.01),
             mis_record!("chr1", Reverse, ThreePrime, 6,  600, 0.01),
 
-        ].into_iter())
+        ])
     }
 
     #[test]