Updating Read Filter documentation

public/java/src/org/broadinstitute/sting/gatk/filters/DuplicateReadFilter.java

@@ -28,11 +28,10 @@ import net.sf.samtools.SAMRecord;
  */
 
 /**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Dec 9, 2009
- *
  * Filter out duplicate reads.
+ *
+ * @author rpoplin
+ * @since Dec 9, 2009
  */
 
 public class DuplicateReadFilter extends ReadFilter {

public/java/src/org/broadinstitute/sting/gatk/filters/FailsVendorQualityCheckFilter.java

@@ -27,11 +27,10 @@ package org.broadinstitute.sting.gatk.filters;
 import net.sf.samtools.SAMRecord;
 
 /**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Jul 19, 2010
+ * Filter out reads that fail the vendor quality check.
  *
- * Filter out FailsVendorQualityCheck reads.
+ * @author rpoplin
+ * @since Jul 19, 2010
  */
 
 public class FailsVendorQualityCheckFilter extends ReadFilter {

public/java/src/org/broadinstitute/sting/gatk/filters/MateSameStrandFilter.java

@@ -3,11 +3,10 @@ package org.broadinstitute.sting.gatk.filters;
 import net.sf.samtools.SAMRecord;
 
 /**
- * Created by IntelliJ IDEA.
- * User: chartl
- * Date: 5/18/11
- * Time: 4:25 PM
- * To change this template use File | Settings | File Templates.
+ * Filter out reads that are not paired, have their mate unmapped, are duplicates, fail vendor quality check or both mate and read are in the same strand.
+ *
+ * @author chartl
+ * @since 5/18/11
  */
 public class MateSameStrandFilter extends ReadFilter {
 

public/java/src/org/broadinstitute/sting/gatk/filters/MaxInsertSizeFilter.java

@@ -4,11 +4,10 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 
 /**
- * Created by IntelliJ IDEA.
- * User: chartl
- * Date: 5/2/11
- * Time: 12:20 PM
- * To change this template use File | Settings | File Templates.
+ * Filter out reads that exceed a given max insert size
+ *
+ * @author chartl
+ * @since 5/2/11
  */
 public class MaxInsertSizeFilter extends ReadFilter {
     @Argument(fullName = "maxInsertSize", shortName = "maxInsert", doc="Discard reads with insert size greater than the specified value, defaults to 1000000", required=false)

public/java/src/org/broadinstitute/sting/gatk/filters/NoOriginalQualityScoresFilter.java

@@ -28,11 +28,10 @@ import net.sf.samtools.SAMRecord;
  */
 
 /**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Nov 19, 2009
+ * Filter out reads that don't have base an original quality quality score tag (usually added by BQSR)
  *
- * Filter out reads that don't have Original Quality scores inside. 
+ * @author rpoplin
+ * @since Nov 19, 2009
  */
 public class NoOriginalQualityScoresFilter extends ReadFilter {
     public boolean filterOut( final SAMRecord read ) {

public/java/src/org/broadinstitute/sting/gatk/filters/NotPrimaryAlignmentFilter.java

@@ -27,11 +27,10 @@ package org.broadinstitute.sting.gatk.filters;
 import net.sf.samtools.SAMRecord;
 
 /**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Dec 9, 2009
- *
  * Filter out duplicate reads.
+ *
+ * @author rpoplin
+ * @since Dec 9, 2009
  */
 
 public class NotPrimaryAlignmentFilter extends ReadFilter {

public/java/src/org/broadinstitute/sting/gatk/filters/PlatformUnitFilter.java

@@ -8,11 +8,10 @@ import java.util.HashSet;
 import java.util.Set;
 
 /**
- * Created by IntelliJ IDEA.
- * User: asivache
- * Date: Sep 21, 2009
- * Time: 2:54:23 PM
- * To change this template use File | Settings | File Templates.
+ * Filter out reads that have blacklisted platform unit tags. (See code documentation for how to create the blacklist).
+ *
+ * @author asivache
+ * @since Sep 21, 2009
  */
 public class PlatformUnitFilter extends ReadFilter {
     // a hack: use static in order to be able to fill it with the data from command line at runtime

public/java/src/org/broadinstitute/sting/gatk/filters/ReadFilter.java

@@ -28,7 +28,6 @@ public abstract class ReadFilter implements SamRecordFilter {
      * @return true if the SAMRecords matches the filter, otherwise false
      * @throws UnsupportedOperationException when paired filter not implemented
      */
-    @Override
     public boolean filterOut(final SAMRecord first, final SAMRecord second) {
         throw new UnsupportedOperationException("Paired filter not implemented: " + this.getClass());
     }

public/java/src/org/broadinstitute/sting/gatk/filters/ReadNameFilter.java

@@ -1,17 +1,13 @@
 package org.broadinstitute.sting.gatk.filters;
 
-import net.sf.samtools.Cigar;
-import net.sf.samtools.CigarElement;
-import net.sf.samtools.CigarOperator;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 
 /**
- * Created by IntelliJ IDEA.
- * User: chartl
- * Date: 9/19/11
- * Time: 4:09 PM
- * To change this template use File | Settings | File Templates.
+ * Filter out all reads except those with this read name
+ *
+ * @author chartl
+ * @since 9/19/11
  */
 public class ReadNameFilter extends ReadFilter {
      @Argument(fullName = "readName", shortName = "rn", doc="Filter out all reads except those with this read name", required=true)

public/java/src/org/broadinstitute/sting/gatk/filters/SampleFilter.java

@@ -31,6 +31,9 @@ import org.broadinstitute.sting.commandline.Argument;
 
 import java.util.Set;
 
+/**
+ * Filter out all reads except those with this sample
+ */
 public class SampleFilter extends ReadFilter {
     @Argument(fullName = "sample_to_keep", shortName = "goodSM", doc="The name of the sample(s) to keep, filtering out all others", required=true)
     private Set SAMPLES_TO_KEEP = null;

public/java/src/org/broadinstitute/sting/gatk/filters/SingleReadGroupFilter.java

@@ -30,11 +30,11 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.commandline.Argument;
 
 /**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Nov 27, 2009
- *
  * Only use reads from the specified read group.
+ *
+ * @author rpoplin
+ * @since Nov 27, 2009
+ *
  */
 
 public class SingleReadGroupFilter extends ReadFilter {

public/java/src/org/broadinstitute/sting/gatk/filters/UnmappedReadFilter.java

@@ -27,11 +27,10 @@ package org.broadinstitute.sting.gatk.filters;
 import net.sf.samtools.SAMRecord;
 
 /**
- * Created by IntelliJ IDEA.
- * User: rpoplin
- * Date: Dec 9, 2009
+ * Filter out unmapped reads.
  *
- * Filter out duplicate reads.
+ * @author rpoplin
+ * @since Dec 9, 2009
  */
 
 public class UnmappedReadFilter extends ReadFilter {