Fix compile errors

broadinstitute · Feb 27, 2015 · 1d575d2 · 1d575d2
1 parent cf2954f
commit 1d575d2
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Showing 4 changed files with 53 additions and 69 deletions.
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/SplitVcfs.java b/src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/SplitVcfs.java
@@ -13,12 +13,12 @@
 import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
-import picard.PicardException;
-import picard.cmdline.CommandLineProgram;
-import picard.cmdline.CommandLineProgramProperties;
-import picard.cmdline.Option;
-import picard.cmdline.StandardOptionDefinitions;
-import picard.cmdline.programgroups.VcfOrBcf;
+import org.broadinstitute.hellbender.cmdline.Argument;
+import org.broadinstitute.hellbender.cmdline.CommandLineProgramProperties;
+import org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram;
+import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
+import org.broadinstitute.hellbender.cmdline.programgroups.VariantProgramGroup;
+import org.broadinstitute.hellbender.exceptions.UserException;
 
 import java.io.File;
 
@@ -34,37 +34,33 @@
                 "headers of the two output files will be identical. An index file is created and a" +
                 "sequence dictionary is required by default.",
         usageShort = "Splits an input VCF or BCF file into two VCF or BCF files",
-        programGroup = VcfOrBcf.class
+        programGroup = VariantProgramGroup.class
 )
-public class SplitVcfs extends CommandLineProgram {
+public class SplitVcfs extends PicardCommandLineProgram {
 
-    @Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc="The VCF or BCF input file")
+    @Argument(shortName = StandardArgumentDefinitions.INPUT_SHORT_NAME, doc = "The VCF or BCF input file")
     public File INPUT;
 
-    @Option(doc = "The VCF or BCF file to which SNP records should be written. The file format is determined by file extension.")
+    @Argument(doc = "The VCF or BCF file to which SNP records should be written. The file format is determined by file extension.")
     public File SNP_OUTPUT;
 
-    @Option(doc = "The VCF or BCF file to which indel records should be written. The file format is determined by file extension.")
+    @Argument(doc = "The VCF or BCF file to which indel records should be written. The file format is determined by file extension.")
     public File INDEL_OUTPUT;
 
-    @Option(shortName = "D", doc = "The index sequence dictionary to use instead of the sequence dictionaries in the input files", optional = true)
+    @Argument(shortName = "D", doc = "The index sequence dictionary to use instead of the sequence dictionaries in the input files", optional = true)
     public File SEQUENCE_DICTIONARY;
 
-    @Option(doc = "If true an exception will be thrown if an event type other than SNP or indel is encountered")
+    @Argument(doc = "If true an exception will be thrown if an event type other than SNP or indel is encountered")
     public Boolean STRICT = true;
 
     private final Log log = Log.getInstance(SplitVcfs.class);
 
-    public static void main(final String[] argv) {
-        new SplitVcfs().instanceMainWithExit(argv);
-    }
-
     public SplitVcfs() {
         this.CREATE_INDEX = true;
     }
 
     @Override
-    protected int doWork() {
+    protected Object doWork() {
         IOUtil.assertFileIsReadable(INPUT);
         final ProgressLogger progress = new ProgressLogger(log, 10000);
 
@@ -76,7 +72,7 @@ protected int doWork() {
                         ? SamReaderFactory.makeDefault().referenceSequence(REFERENCE_SEQUENCE).getFileHeader(SEQUENCE_DICTIONARY).getSequenceDictionary()
                         : fileHeader.getSequenceDictionary();
         if (CREATE_INDEX && sequenceDictionary == null) {
-            throw new PicardException("A sequence dictionary must be available (either through the input file or by setting it explicitly) when creating indexed output.");
+            throw new UserException("A sequence dictionary must be available (either through the input file or by setting it explicitly) when creating indexed output.");
         }
 
         final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
@@ -114,6 +110,6 @@ protected int doWork() {
         snpWriter.close();
         indelWriter.close();
 
-        return 0;
+        return null;
     }
 }
diff --git a/...main/java/org/broadinstitute/hellbender/tools/picard/vcf/UpdateVcfSequenceDictionary.java b/...main/java/org/broadinstitute/hellbender/tools/picard/vcf/UpdateVcfSequenceDictionary.java
@@ -36,11 +36,11 @@
 import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
-import picard.cmdline.CommandLineProgram;
-import picard.cmdline.CommandLineProgramProperties;
-import picard.cmdline.Option;
-import picard.cmdline.StandardOptionDefinitions;
-import picard.cmdline.programgroups.VcfOrBcf;
+import org.broadinstitute.hellbender.cmdline.Argument;
+import org.broadinstitute.hellbender.cmdline.CommandLineProgramProperties;
+import org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram;
+import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
+import org.broadinstitute.hellbender.cmdline.programgroups.VariantProgramGroup;
 
 import java.io.File;
 
@@ -53,27 +53,23 @@
 @CommandLineProgramProperties(
         usage = "Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.",
         usageShort = "Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.",
-        programGroup = VcfOrBcf.class
+        programGroup = VariantProgramGroup.class
 )
-public class UpdateVcfSequenceDictionary extends CommandLineProgram {
-     @Option(shortName = StandardOptionDefinitions.INPUT_SHORT_NAME, doc = "Input VCF")
+public class UpdateVcfSequenceDictionary extends PicardCommandLineProgram {
+     @Argument(shortName = StandardArgumentDefinitions.INPUT_SHORT_NAME, doc = "Input VCF")
     public File INPUT;
 
-    @Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "Output VCF to be written.")
+    @Argument(shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, doc = "Output VCF to be written.")
     public File OUTPUT;
 
-    @Option(shortName = StandardOptionDefinitions.SEQUENCE_DICTIONARY_SHORT_NAME, doc = "A Sequence Dictionary (can be read from one of the " +
+    @Argument(shortName = StandardArgumentDefinitions.SEQUENCE_DICTIONARY_SHORT_NAME, doc = "A Sequence Dictionary (can be read from one of the " +
             "following file types (SAM, BAM, VCF, BCF, Interval List, Fasta, or Dict)")
     public File SEQUENCE_DICTIONARY;
 
     private final Log log = Log.getInstance(UpdateVcfSequenceDictionary.class);
 
-    public static void main(final String[] args) {
-        new UpdateVcfSequenceDictionary().instanceMainWithExit(args);
-    }
-
     @Override
-    protected int doWork() {
+    protected Object doWork() {
         IOUtil.assertFileIsReadable(INPUT);
         IOUtil.assertFileIsReadable(SEQUENCE_DICTIONARY);
         IOUtil.assertFileIsWritable(OUTPUT);
@@ -105,6 +101,6 @@ protected int doWork() {
         CloserUtil.close(fileReader);
         vcfWriter.close();
 
-        return 0;
+        return null;
     }
 }
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/VcfFormatConverter.java b/src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/VcfFormatConverter.java
@@ -37,12 +37,12 @@
 import htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder;
 import htsjdk.variant.vcf.VCFFileReader;
 import htsjdk.variant.vcf.VCFHeader;
-import picard.PicardException;
-import picard.cmdline.CommandLineProgram;
-import picard.cmdline.CommandLineProgramProperties;
-import picard.cmdline.Option;
-import picard.cmdline.StandardOptionDefinitions;
-import picard.cmdline.programgroups.VcfOrBcf;
+import org.broadinstitute.hellbender.cmdline.Argument;
+import org.broadinstitute.hellbender.cmdline.CommandLineProgramProperties;
+import org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram;
+import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
+import org.broadinstitute.hellbender.cmdline.programgroups.VariantProgramGroup;
+import org.broadinstitute.hellbender.exceptions.UserException;
 
 import java.io.File;
 
@@ -55,31 +55,27 @@
         usage = "Convert a VCF file to a BCF file, or BCF to VCF.\n" +
                 "Input and output formats are determined by file extension.",
         usageShort = "Converts a VCF file to a BCF file, or BCF to VCF",
-        programGroup = VcfOrBcf.class
+        programGroup = VariantProgramGroup.class
 )
-public class VcfFormatConverter extends CommandLineProgram {
+public class VcfFormatConverter extends PicardCommandLineProgram {
     // The following attributes define the command-line arguments
     public static final Log LOG = Log.getInstance(VcfFormatConverter.class);
 
-    @Option(doc="The BCF or VCF input file. The file format is determined by file extension.", shortName= StandardOptionDefinitions.INPUT_SHORT_NAME)
+    @Argument(doc = "The BCF or VCF input file. The file format is determined by file extension.", shortName = StandardArgumentDefinitions.INPUT_SHORT_NAME)
     public File INPUT;
 
-    @Option(doc="The BCF or VCF output file. The file format is determined by file extension.", shortName=StandardOptionDefinitions.OUTPUT_SHORT_NAME)
+    @Argument(doc = "The BCF or VCF output file. The file format is determined by file extension.", shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME)
     public File OUTPUT;
 
-	@Option(doc="Fail if an index is not available for the input VCF/BCF")
+	@Argument(doc = "Fail if an index is not available for the input VCF/BCF")
 	public Boolean REQUIRE_INDEX = true;
 
-    public static void main(final String[] argv) {
-        new VcfFormatConverter().instanceMainWithExit(argv);
-    }
-
 	public VcfFormatConverter() {
 		this.CREATE_INDEX = true;
 	}
 
     @Override
-    protected int doWork() {
+    protected Object doWork() {
         final ProgressLogger progress = new ProgressLogger(LOG, 10000);
 
         IOUtil.assertFileIsReadable(INPUT);
@@ -89,7 +85,7 @@ protected int doWork() {
 	    final VCFHeader header = new VCFHeader(reader.getFileHeader());
 	    final SAMSequenceDictionary sequenceDictionary = header.getSequenceDictionary();
 	    if (CREATE_INDEX && sequenceDictionary == null) {
-		    throw new PicardException("A sequence dictionary must be available in the input file when creating indexed output.");
+		    throw new UserException("A sequence dictionary must be available in the input file when creating indexed output.");
 	    }
 
         final VariantContextWriterBuilder builder = new VariantContextWriterBuilder()
@@ -113,6 +109,6 @@ protected int doWork() {
 	    CloserUtil.close(reader);
         writer.close();
 
-        return 0;
+        return null;
     }
 }
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/VcfToIntervalList.java b/src/main/java/org/broadinstitute/hellbender/tools/picard/vcf/VcfToIntervalList.java
@@ -4,11 +4,11 @@
 import htsjdk.samtools.util.IntervalList;
 import htsjdk.samtools.util.Log;
 import htsjdk.variant.vcf.VCFFileReader;
-import picard.cmdline.CommandLineProgram;
-import picard.cmdline.CommandLineProgramProperties;
-import picard.cmdline.Option;
-import picard.cmdline.StandardOptionDefinitions;
-import picard.cmdline.programgroups.VcfOrBcf;
+import org.broadinstitute.hellbender.cmdline.Argument;
+import org.broadinstitute.hellbender.cmdline.CommandLineProgramProperties;
+import org.broadinstitute.hellbender.cmdline.PicardCommandLineProgram;
+import org.broadinstitute.hellbender.cmdline.StandardArgumentDefinitions;
+import org.broadinstitute.hellbender.cmdline.programgroups.VariantProgramGroup;
 
 import java.io.File;
 
@@ -21,30 +21,26 @@
 @CommandLineProgramProperties(
         usage = "Converts a VCF or BCF file to a Picard Interval List.",
         usageShort = "Converts a VCF or BCF file to a Picard Interval List.",
-        programGroup = VcfOrBcf.class
+        programGroup = VariantProgramGroup.class
 )
-public class VcfToIntervalList extends CommandLineProgram {
+public class VcfToIntervalList extends PicardCommandLineProgram {
     // The following attributes define the command-line arguments
     public static final Log LOG = Log.getInstance(VcfToIntervalList.class);
 
-    @Option(doc="The BCF or VCF input file. The file format is determined by file extension.", shortName= StandardOptionDefinitions.INPUT_SHORT_NAME)
+    @Argument(doc = "The BCF or VCF input file. The file format is determined by file extension.", shortName= StandardArgumentDefinitions.INPUT_SHORT_NAME)
     public File INPUT;
 
-    @Option(shortName = StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc = "The output Picard Interval List")
+    @Argument(shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, doc = "The output Picard Interval List")
     public File OUTPUT;
 
-    public static void main(final String[] argv) {
-        new VcfToIntervalList().instanceMainWithExit(argv);
-    }
-
     @Override
-    protected int doWork() {
+    protected Object doWork() {
         IOUtil.assertFileIsReadable(INPUT);
         IOUtil.assertFileIsWritable(OUTPUT);
 
         final IntervalList intervalList = VCFFileReader.fromVcf(INPUT);
         // Sort and write the output
         intervalList.uniqued().write(OUTPUT);
-        return 0;
+        return null;
     }
 }