Merge pull request #7 from compgen-io/phasing

Phasing

build.xml

@@ -1,5 +1,5 @@
 <project name="ngsutilsj" default="jar">
-    <property name="version" value="0.4.15"/>
+    <property name="version" value="0.4.17"/>
     <property name="build" value="dev"/>
     <property name="lib.dir" value="lib"/>
     <property name="blib.dir" value="blib"/>

src/java/io/compgen/ngsutils/NGSUtils.java

@@ -25,6 +25,7 @@
 import io.compgen.ngsutils.cli.bam.BamExtract;
 import io.compgen.ngsutils.cli.bam.BamFilterCli;
 import io.compgen.ngsutils.cli.bam.BamFlagDuplicates;
+import io.compgen.ngsutils.cli.bam.BamPhase;
 import io.compgen.ngsutils.cli.bam.BamReadGroup;
 import io.compgen.ngsutils.cli.bam.BamRefCount;
 import io.compgen.ngsutils.cli.bam.BamRemoveClipping;
@@ -35,6 +36,7 @@
 import io.compgen.ngsutils.cli.bam.BamToBed;
 import io.compgen.ngsutils.cli.bam.BamToBedGraph;
 import io.compgen.ngsutils.cli.bam.BamToBedPE;
+import io.compgen.ngsutils.cli.bam.BamToFasta;
 import io.compgen.ngsutils.cli.bam.BamToFastq;
 import io.compgen.ngsutils.cli.bam.BinCount;
 import io.compgen.ngsutils.cli.bam.PileupCli;
@@ -52,6 +54,7 @@
 import io.compgen.ngsutils.cli.fasta.FastaFilter;
 import io.compgen.ngsutils.cli.fasta.FastaGC;
 import io.compgen.ngsutils.cli.fasta.FastaGenerateReads;
+import io.compgen.ngsutils.cli.fasta.FastaGrep;
 import io.compgen.ngsutils.cli.fasta.FastaMask;
 import io.compgen.ngsutils.cli.fasta.FastaNames;
 import io.compgen.ngsutils.cli.fasta.FastaPWM;
@@ -93,6 +96,7 @@
 import io.compgen.ngsutils.cli.vcf.VCFToBED;
 import io.compgen.ngsutils.cli.vcf.VCFToBEDPE;
 import io.compgen.ngsutils.cli.vcf.VCFToCount;
+import io.compgen.ngsutils.cli.vcf.VCFPeptide;
 import io.compgen.ngsutils.cli.vcf.VCFTsTvRatio;
 import io.compgen.ngsutils.support.DigestCmd;
 import io.compgen.ngsutils.support.stats.FisherCli;
@@ -208,7 +212,11 @@ public static void main(String[] args) {
 			.addCommand(VCFCheck.class)
 			.addCommand(BamToBedPE.class)
 			.addCommand(BedPEToBed.class)
-			.addCommand(BamClean.class);
+			.addCommand(BamClean.class)
+			.addCommand(VCFPeptide.class)
+			.addCommand(FastaGrep.class)
+			.addCommand(BamToFasta.class)
+			.addCommand(BamPhase.class)
 
         try {
             if (args.length == 0) {
@@ -237,11 +245,12 @@ public static void main(String[] args) {
         } catch (UnknownArgumentException e) {
             System.err.println("ERROR: " + e.getMessage());
             System.err.println();
-            System.exit(1);
             try {
                 main.showCommandHelp(e.clazz);
             } catch (MissingCommandException e1) {
             }
+            System.exit(1);
+
         } catch (Exception e) {
             e.printStackTrace();
             System.exit(1);