Help message, classifier class checking, and some feature computer ex…

…clusion
abrari · Jul 27, 2015 · fdd1f71 · fdd1f71
1 parent addff66
commit fdd1f71
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Showing 2 changed files with 42 additions and 11 deletions.
diff --git a/src/gpsnp/app/Main.java b/src/gpsnp/app/Main.java
@@ -166,6 +166,11 @@ public static void callSNPs(File inputBAM,
 
     public static void main(String[] argv) {
 
+        if (argv.length == 0) {
+            printHelp();
+            return;
+        }
+
         ArgParser args = new ArgParser(argv);
 
         String referencePath;
@@ -181,6 +186,16 @@ public static void main(String[] argv) {
             classifierClass = getRequiredStringArg(args, "-C", "Missing required argument for classifier class, use -C");
         } catch (Exception e1) {
             System.err.println(e1.getMessage());
+            System.out.println("---");
+            printHelp();
+            return;
+        }
+
+        // Check classifier class exists
+        try {
+            Class.forName("gpsnp.classifier." + classifierClass);
+        } catch (ClassNotFoundException e) {
+            System.err.println("Invalid classifier class: " + classifierClass + "\nUse either SeSpRuleClassifier or PrRcRuleClassifier");
             return;
         }
 
@@ -247,4 +262,19 @@ public static void main(String[] argv) {
         }
     }
 
+    public static void printHelp() {
+        System.out.println("SNP calling program version 0.1");
+        System.out.println("Required arguments:");
+        System.out.println("    -R        reference file path (.fasta)");
+        System.out.println("    -B        input BAM file (.bam)");
+        System.out.println("    -V        output variant file (.vcf)");
+        System.out.println("    -C        classifier class (SeSpRuleClassifier or PrRcRuleClassifier)");
+        System.out.println("Optional arguments:");
+        System.out.println("    -t [4]    number of threads to run");
+        System.out.println("    -q [1.0]  minimum Phred-scaled quality to report variant");
+        System.out.println("    -d [2]    minimum total depth to examine for variant");
+        System.out.println("    -v [2]    minimum reads with variant allele required for variant calling");
+        System.out.println("    -phred33  the input BAM is in Phred+33 scoring");
+    }
+
 }
diff --git a/src/gpsnp/featureComputer/FeatureList.java b/src/gpsnp/featureComputer/FeatureList.java
@@ -35,23 +35,24 @@ public static List<FeatureComputer> getFeatures() {
         return computers;
     }
 
+    // Exclude features that don't exists in the rule set
     public static List<FeatureComputer> getFeatures(boolean isPhred33) {
         List<FeatureComputer> computers = new ArrayList<FeatureComputer>();
-        computers.add(new TsTvComputer());
+        // computers.add(new TsTvComputer());
         computers.add(new MaxQualAlleleComputer(isPhred33));
         computers.add(new MeanQualAlleleComputer(isPhred33));
-        computers.add(new RelativeDistanceComputer());
+        // computers.add(new RelativeDistanceComputer());
         computers.add(new DepthComputer());
-        computers.add(new AlignmentQualityComputer());
-        computers.add(new ErrorProbComputer());
-        computers.add(new DinucRepeatCounter());
-        computers.add(new StrandBiasComputer());
-        computers.add(new AreaMismatchComputer());
-        computers.add(new HomopolymerRunComputer());
-        computers.add(new NucDiversityComputer());
-        computers.add(new MismatchComputer());
+        // computers.add(new AlignmentQualityComputer());
+        // computers.add(new ErrorProbComputer());
+        // computers.add(new DinucRepeatCounter());
+        // computers.add(new StrandBiasComputer());
+        // computers.add(new AreaMismatchComputer());
+        // computers.add(new HomopolymerRunComputer());
+        // computers.add(new NucDiversityComputer());
+        // computers.add(new MismatchComputer());
         computers.add(new AlleleBalanceComputer());
-        computers.add(new NearbyQualComputer(isPhred33));
+        // computers.add(new NearbyQualComputer(isPhred33));
 
         return computers;
     }