Option dash (#8)

* Added makefile to make my life easier

* Now getting onejar-maven-plugin from com.jolira

* Added -dash for a '-' rather than reference bases

* Inc version to 0.4

README.md

@@ -1,7 +1,7 @@
 <p align="center">
   <img src="https://github.com/armintoepfer/ConsensusFixer/blob/master/CF_logo.png?raw=true" alt="ConsensusFixer logo"/>
 </p>
-<h1 align="center"><b>C</b>onsensus<b>F</b>ixer <b>0.3</b></h1>
+<h1 align="center"><b>C</b>onsensus<b>F</b>ixer <b>0.4</b></h1>
 
 ***
 
@@ -21,6 +21,7 @@ Please get the latest binary at [releases](https://github.com/cbg-ethz/Consensus
 ### FEATURES:
  - Calls consensus sequence with a minimal coverage `-mcc INT`
  - Integrates consensus sequence into given reference `-r ref.fasta`
+ - Optionally insert dashes '-' instead of bases from the reference.
  - Include insertions with a minimal coverage of `-mic INT`
  - Optionally, only include in-frame insertions `-f`
  - Calls amibiguous bases (wobbles) if relative base abundance is above `-plurality DOUBLE`
@@ -57,6 +58,7 @@ Please open an issue on github
   -m                 : Majority vote respecting pluralityN first, otherwise allow wobbles.
   -f                 : Only allow in frame insertions.
   -d                 : Remove gaps if they are >= pluralityN.
+  -dash              : Use '-' instead of bases from the reference.
   -s                 : Single core mode with low memory footprint.
 ```
 

makefile

@@ -0,0 +1,7 @@
+all:a
+	mvn clean package
+
+a:
+	mvn -DartifactId=samtools -DgroupId=net.sf -Dversion=1.9.6 -Dpackaging=jar -Dfile=src/main/resources/jars/sam-1.96.jar -DgeneratePom=false install:install-file
+
+

pom.xml

@@ -4,7 +4,7 @@
 
     <groupId>ch.ethz.bsse</groupId>
     <artifactId>consensusfixer</artifactId>
-    <version>0.3</version>
+    <version>0.4</version>
     <packaging>jar</packaging>
     <name>ConsensusFixer</name>
 
@@ -52,7 +52,7 @@
                 </configuration>
             </plugin>
             <plugin>
-                <groupId>org.dstovall</groupId>
+                <groupId>com.jolira</groupId>
                 <artifactId>onejar-maven-plugin</artifactId>
                 <version>1.4.4</version>
                 <executions>

src/main/java/ch/ethz/bsse/cf/Startup.java

@@ -76,6 +76,8 @@ public static void main(String[] args) throws IOException {
     private boolean progressiveInsertion;
     @Option(name = "-pis")
     private int progressiveInsertionSize = 300;
+    @Option(name = "-dash")
+    private boolean dashForReference = false;
 
     private void setInputOutput() {
         if (output == null) {
@@ -106,6 +108,7 @@ private void setMainParameters() {
         Globals.MAXIMUM_INSERTION = this.maximumInsertion;
         Globals.PROGRESSIVE_INSERTION = this.progressiveInsertion;
         Globals.PROGRESSIVE_INSERTION_SIZE = this.progressiveInsertionSize;
+        Globals.INSERT_DASHES_FOR_REFERENCE = this.dashForReference;
         StatusUpdate.SILENT = this.silent;
     }
 
@@ -186,6 +189,7 @@ public void doMain(String[] args) throws IOException {
             System.err.println("  -mi \t\t\t: Only the insertion with the maximum frequency greater than mic is incorporated.");
             System.err.println("  -pi \t\t\t: Progressive insertion mode, respecting mic.");
             System.err.println("  -pis INT\t\t: Window size for progressive insertion mode (default: 300).");
+            System.err.println("  -dash \t\t: Use '-' instead of bases from the reference.");
             System.err.println("  -s \t\t\t: Single core mode with low memory footprint.");
             System.err.println("");
             System.err.println(" -------------------------");

src/main/java/ch/ethz/bsse/cf/informationholder/Globals.java

@@ -45,6 +45,7 @@ public class Globals {
     public static int MIN_CONS_COV;
     public static int MIN_INS_COV;
     public static int PROGRESSIVE_INSERTION_SIZE;
+    public static boolean INSERT_DASHES_FOR_REFERENCE;
     public static char[] GENOME;
     public static final Map<Integer, Map<Integer, Integer>> DELETION_MAP_PASSES = new ConcurrentHashMap<>();
     public static final Map<Integer, AtomicLongMap> DELETION_MAP = new ConcurrentHashMap<>();

src/main/java/ch/ethz/bsse/cf/utils/Alignment.java

@@ -143,7 +143,11 @@ public static void saveConsensus() {
                 if (Globals.CONSENSUS_MAP.containsKey(i)) {
                     consensusSequence.append(Globals.CONSENSUS_MAP.get(i));
                 } else {
-                    consensusSequence.append(Globals.GENOME[i]);
+                    if (Globals.INSERT_DASHES_FOR_REFERENCE){
+                        consensusSequence.append('-');
+                    } else {
+                        consensusSequence.append(Globals.GENOME[i]);
+                    }
                 }
                 if (insertionMap.containsKey(i) && !insertionMap.get(i).isEmpty()) {
                     if (Globals.MAXIMUM_INSERTION) {