Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable

protected/java/src/org/broadinstitute/sting/gatk/walkers/compression/reducereads/CompareBAM.java

@@ -1,6 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.compression.reducereads;
 
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.DuplicateReadFilter;
@@ -11,6 +12,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
 import org.broadinstitute.sting.gatk.walkers.ReadFilters;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -39,6 +41,7 @@ import java.util.Map;
  * @since 10/30/11
  */
 
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @ReadFilters({UnmappedReadFilter.class,NotPrimaryAlignmentFilter.class,DuplicateReadFilter.class,FailsVendorQualityCheckFilter.class})
 public class CompareBAM extends LocusWalker<Map<CompareBAM.TestName, Boolean>, CompareBAM.TestResults> {
     @Argument(required = true,  shortName = "rr",  fullName = "reduced_readgroup", doc = "The read group ID corresponding to the compressed BAM being tested") public String reducedReadGroupID;

protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java

@@ -29,6 +29,7 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -42,6 +43,7 @@ import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
@@ -80,6 +82,7 @@ import java.util.*;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Variant Evaluation and Manipulation Tools", extraDocs = {CommandLineGATK.class} )
 @Reference(window=@Window(start=-HaplotypeResolver.ACTIVE_WINDOW,stop= HaplotypeResolver.ACTIVE_WINDOW))
 public class HaplotypeResolver extends RodWalker<Integer, Integer> {
 

public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java

@@ -29,11 +29,13 @@ import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.util.Iterator;
@@ -46,6 +48,7 @@ import java.util.Iterator;
  * @author mhanna
  * @version 0.1
  */
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
 public class AlignmentValidation extends ReadWalker<Integer,Integer> {
     /**
      * The supporting BWT index generated using BWT. 

public/java/src/org/broadinstitute/sting/alignment/AlignmentWalker.java

@@ -34,11 +34,13 @@ import org.broadinstitute.sting.alignment.bwa.BWTFiles;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.File;
@@ -50,6 +52,7 @@ import java.io.File;
  * @author mhanna
  * @version 0.1
  */
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @WalkerName("Align")
 public class AlignmentWalker extends ReadWalker<Integer,Integer> {
     @Argument(fullName="target_reference",shortName="target_ref",doc="The reference to which reads in the source file should be aligned.  Alongside this reference should sit index files " +

public/java/src/org/broadinstitute/sting/alignment/CountBestAlignments.java

@@ -30,9 +30,11 @@ import org.broadinstitute.sting.alignment.bwa.BWTFiles;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 
 import java.io.PrintStream;
@@ -48,6 +50,7 @@ import java.util.TreeMap;
  * @author mhanna
  * @version 0.1
  */
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
 public class CountBestAlignments extends ReadWalker<Integer,Integer> {
     /**
      * The supporting BWT index generated using BWT.

public/java/src/org/broadinstitute/sting/gatk/CommandLineGATK.java

@@ -131,6 +131,12 @@ public class CommandLineGATK extends CommandLineExecutable {
         // can't close tribble index when writing
         if ( message.indexOf("Unable to close index for") != -1 )
             exitSystemWithUserError(new UserException(t.getCause().getMessage()));
+
+        // disk is full
+        if ( message.indexOf("No space left on device") != -1 )
+            exitSystemWithUserError(new UserException(t.getMessage()));
+        if ( t.getCause().getMessage().indexOf("No space left on device") != -1 )
+            exitSystemWithUserError(new UserException(t.getCause().getMessage()));
     }
 
     /**

public/java/src/org/broadinstitute/sting/gatk/examples/CoverageBySample.java

@@ -3,10 +3,12 @@ package org.broadinstitute.sting.gatk.examples;
 
 import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
@@ -17,8 +19,9 @@ import java.util.List;
 import java.util.Map;
 
 /**
- * Computes the coverage per sample.
+ * Computes the coverage per sample for every position (use with -L argument!).
  */
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
 public class CoverageBySample extends LocusWalker<Integer, Integer> {
     @Output
     protected PrintStream out;    

public/java/src/org/broadinstitute/sting/gatk/examples/GATKPaperGenotyper.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.examples;
 
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -35,6 +36,7 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.DiploidGenotype;
 import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.io.PrintStream;
@@ -46,6 +48,7 @@ import java.io.PrintStream;
  *
  * @author aaron
  */
+@DocumentedGATKFeature( groupName = "Variant Discovery Tools", extraDocs = {CommandLineGATK.class} )
 public class GATKPaperGenotyper extends LocusWalker<Integer,Long> implements TreeReducible<Long> {
     // the possible diploid genotype strings
     private static enum GENOTYPE { AA, AC, AG, AT, CC, CG, CT, GG, GT, TT }

public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java

@@ -27,6 +27,7 @@ package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
 import net.sf.picard.util.PeekableIterator;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -36,6 +37,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.variantcontext.*;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
 
@@ -80,6 +82,7 @@ import java.util.*;
  * @author Mauricio Carneiro, Roger Zurawicki
  * @since 5/8/12
  */
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @By(value = DataSource.READS)
 @PartitionBy(PartitionType.INTERVAL)
 public class DiagnoseTargets extends LocusWalker<Long, Long> {

public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/FindCoveredIntervals.java

@@ -25,6 +25,7 @@
 package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
 
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -33,9 +34,11 @@ import org.broadinstitute.sting.gatk.walkers.ActiveRegionWalker;
 import org.broadinstitute.sting.gatk.walkers.PartitionBy;
 import org.broadinstitute.sting.gatk.walkers.PartitionType;
 import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
 import java.io.PrintStream;
 
+@DocumentedGATKFeature( groupName = "BAM Processing and Analysis Tools", extraDocs = {CommandLineGATK.class} )
 @PartitionBy(PartitionType.CONTIG)
 @ActiveRegionExtension(extension = 0, maxRegion = 50000)
 public class FindCoveredIntervals extends ActiveRegionWalker<GenomeLoc, Long> {

public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java

@@ -26,17 +26,20 @@
 package org.broadinstitute.sting.gatk.walkers.fasta;
 
 import org.broadinstitute.sting.commandline.Output;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
 import java.io.PrintStream;
 
 /**
  * Calculates basic statistics about the reference sequence itself
  */
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
 public class FastaStats extends RefWalker<Byte, FastaStats.FastaStatistics> {
     @Output PrintStream out;
 

public/java/src/org/broadinstitute/sting/gatk/walkers/qc/CountRODs.java

@@ -32,6 +32,7 @@ import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
@@ -42,6 +43,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
 import java.io.PrintStream;
 import java.util.*;
@@ -70,6 +72,7 @@ import java.util.*;
  * </pre>
  *
  */
+@DocumentedGATKFeature( groupName = "Quality Control and Simple Analysis Tools", extraDocs = {CommandLineGATK.class} )
 public class CountRODs extends RodWalker<CountRODs.Datum, Pair<ExpandingArrayList<Long>, Long>> implements TreeReducible<Pair<ExpandingArrayList<Long>, Long>> {
     @Output
     public PrintStream out;