From 71aa0e94ed0966976f14c5905b8f42418c342f36 Mon Sep 17 00:00:00 2001
From: mikesh <mikhail.shugay@gmail.com>
Date: Tue, 17 Feb 2015 17:59:15 +0300
Subject: [PATCH] Some refactoring

---
 .../oncomigec/core/correct/CorrectorParameters.java    |  4 ++--
 .../com/milaboratory/oncomigec/pipeline/MigecCli.java  | 10 +++++-----
 .../preproc/demultiplex/barcode/BarcodeSearcher.java   |  2 +-
 3 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorParameters.java b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorParameters.java
index a7794d0..9d4f478 100644
--- a/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorParameters.java
+++ b/src/main/java/com/milaboratory/oncomigec/core/correct/CorrectorParameters.java
@@ -73,7 +73,7 @@ public double getMaxBasePairsMaskedRatio() {
     public Element toXml() {
         Element e = new Element("CorrectorParameters");
         e.addContent(new Element("classifierProbabilityThreshold").setText(Double.toString(classifierProbabilityThreshold)));
-        e.addContent(new Element("filterSingleMigs").setText(Boolean.toString(filterSingletons)));
+        e.addContent(new Element("filterSingletons").setText(Boolean.toString(filterSingletons)));
         e.addContent(new Element("singletonFilterRatio").setText(Double.toString(singletonFilterRatio)));
         e.addContent(new Element("minMigCoverage").setText(Integer.toString(minMigCoverage)));
         e.addContent(new Element("minMigCount").setText(Integer.toString(minMigCount)));
@@ -86,7 +86,7 @@ public static CorrectorParameters fromXml(Element parent) {
         Element e = parent.getChild("CorrectorParameters");
         return new CorrectorParameters(
                 Double.parseDouble(e.getChildTextTrim("classifierProbabilityThreshold")),
-                Boolean.parseBoolean(e.getChildTextTrim("filterSingleMigs")),
+                Boolean.parseBoolean(e.getChildTextTrim("filterSingletons")),
                 Double.parseDouble(e.getChildTextTrim("singletonFilterRatio")),
                 Integer.parseInt(e.getChildTextTrim("minMigCoverage")),
                 Integer.parseInt(e.getChildTextTrim("minMigCount")),
diff --git a/src/main/java/com/milaboratory/oncomigec/pipeline/MigecCli.java b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecCli.java
index 398552a..bb0b9b2 100644
--- a/src/main/java/com/milaboratory/oncomigec/pipeline/MigecCli.java
+++ b/src/main/java/com/milaboratory/oncomigec/pipeline/MigecCli.java
@@ -81,7 +81,7 @@ public static void main(String[] args) throws Exception {
                         OptionBuilder
                                 .withArgName("name")
                                 .hasArg(true)
-                                .withDescription("name of MIGEC parameter preset " +
+                                .withDescription("name of OncoMIGEC parameter preset " +
                                         "(currently Illumina-Exome or Torrent454-Exome, case-insensitive)")
                                 .withLongOpt(OPT_LOAD_PRESET)
                                 .create()
@@ -90,7 +90,7 @@ public static void main(String[] args) throws Exception {
                         OptionBuilder
                                 .withArgName("file")
                                 .hasArg(true)
-                                .withDescription("MIGEC2 parameter file in XML format")
+                                .withDescription("OncoMIGEC parameter file in XML format")
                                 .withLongOpt(OPT_IMPORT_PRESET)
                                 .create()
                 )
@@ -226,7 +226,7 @@ public static void main(String[] args) throws Exception {
 
             // version
             if (commandLine.hasOption(OPT_VERSION_SHORT)) {
-                System.out.println("You are using MIGEC2 pipeline of version " + MY_VERSION);
+                System.out.println("You are using OncoMIGEC pipeline of version " + MY_VERSION);
                 System.exit(0);
             }
 
@@ -461,7 +461,7 @@ private static void checkPreprocess(MigecPipeline pipeline, File outputFolder,
 
     private static void runFirstStage(MigecPipeline pipeline, File outputFolder) {
         try {
-            print2("Running first stage of MiGEC");
+            print2("Running first stage of OncoMiGEC");
             pipeline.runFirstStage();
         } catch (Exception e) {
             System.err.println("Error on first stage of analysis: " + e.toString());
@@ -491,7 +491,7 @@ private static void dumpVariants(MigecPipeline pipeline, File outputFolder, doub
 
     private static void runSecondStage(MigecPipeline pipeline, File outputFolder) {
         try {
-            print2("Running second stage of MiGEC");
+            print2("Running second stage of OncoMiGEC");
             pipeline.runSecondStage();
         } catch (Exception e) {
             System.err.println("Error on second stage of analysis: " + e.toString());
diff --git a/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcher.java b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcher.java
index 9e6738f..45fc9de 100644
--- a/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcher.java
+++ b/src/main/java/com/milaboratory/oncomigec/preproc/demultiplex/barcode/BarcodeSearcher.java
@@ -69,7 +69,7 @@ private static String charToRegex(char c) {
             case 'N':
                 return "[ATGC]";
             default:
-                throw new IllegalArgumentException("Illegar nucleotide character");
+                throw new IllegalArgumentException("Illegal nucleotide character");
         }
     }