Update references to old-style arguments (#5063)

* Fixing references to old style arguments that were still in documentation and error messages.

src/main/java/org/broadinstitute/hellbender/tools/FixCallSetSampleOrdering.java

@@ -175,7 +175,7 @@ private Map<Path, String> loadGvcfToHeaderSampleMap() {
 
             if ( ! gvcfPathsFromSampleNameMap.isEmpty() ) {
                 throw new SampleNameFixingCannotProceedException("Not all GVCF paths from the --" + GenomicsDBImport.SAMPLE_NAME_MAP_LONG_NAME +
-                        " were found in the provided --gvcfToHeaderSampleMapFile");
+                        " were found in the provided --gvcf-to-header-sample-map-file");
             }
 
             return mapping;
@@ -273,11 +273,11 @@ private void assertThatTheyReallyWantToProceed(){
                                 "You should be certain you want to do this before proceeding.\n" +
                                 "If the following description does not apply to your VCF then the newly generated vcf will be \n\n \t\tHORRIBLY CORRUPTED: by having its sample names shuffled so that the genotypes don't correspond to the correct samples\n\n" +
                                 "1: your vcf was generated using a GenomicsDBImport released before gatk version 4.beta.6\n" +
-                                "2: you set --batchSize != 0 when running GenomicsDBImport\n" +
+                                "2: you set --batch-size != 0 when running GenomicsDBImport\n" +
                                 "3: your callset was imported in multiple batches, i.e. your number of samples > batchSize\n" +
                                 "4: you supplied the exact same sampleNameMap file and batch size you used in the initial GenomicsDBImport\n" +
                                 "or:\n" +
-                                "1. you ran GenomicsDBImport with --readerThreads > 1, and at least one sample name as declared\n" +
+                                "1. you ran GenomicsDBImport with --reader-threads > 1, and at least one sample name as declared\n" +
                                 "   in a GVCF header did not match the sample name specified for that file in the sample name map file\n" +
                                 "   provided to GenomicsDBImport\n\n" +
 

src/main/java/org/broadinstitute/hellbender/tools/HaplotypeCallerSpark.java

@@ -62,7 +62,7 @@
  *
  * <p>This is an implementation of {@link HaplotypeCaller} using spark to distribute the computation.
  * It is still in an early stage of development and does not yet support all the options that the non-spark version does.
- * Specifically it does not support the --dbsnp, --comp, and --bamOutput options.</p>
+ * Specifically it does not support the --dbsnp, --comp, and --bam-output options.</p>
  *
  * <h3>Usage Example</h3>
  * <pre>

src/main/java/org/broadinstitute/hellbender/tools/spark/ApplyBQSRSpark.java

@@ -42,7 +42,8 @@
  * gatk ApplyBQSRSpark \
  * -I gs://my-gcs-bucket/input.bam \
  * -bqsr gs://my-gcs-bucket/recalibration.table \
- * -SQQ 10 -SQQ 20 -SQQ 30 -SQQ 40 \
+ * --static-quantized-quals 10 --static-quantized-quals 20 \
+ * --static-quantized-quals 30 --static-quantized-quals 40 \
  * -O gs://my-gcs-bucket/output.bam \
  * -- \
  * --sparkRunner GCS \

src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/PSFilterArgumentCollection.java

@@ -291,10 +291,10 @@ public void doReadFilterArgumentWarnings(final GATKReadFilterPluginDescriptor pl
         for (final ReadFilter filter : readFilters) {
             if (filter.getClass().isAssignableFrom(AmbiguousBaseReadFilter.class)) {
                 logger.warn("Detected the use of AmbiguousBaseReadFilter, which is applied before the PathSeq " +
-                        "base masking steps. Did you mean to use --maxMaskedBases, which is applied after masking?");
+                        "base masking steps. Did you mean to use --max-masked-bases, which is applied after masking?");
             } else if (filter.getClass().isAssignableFrom(ReadLengthReadFilter.class)) {
                 logger.warn("Detected the use of ReadLengthReadFilter, which is applied before the PathSeq " +
-                        "clipping steps. Did you mean to use --minClippedReadLength, which is applied after clipping?");
+                        "clipping steps. Did you mean to use --min-clipped-read-length, which is applied after clipping?");
             }
         }
     }

src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/PSScorer.java

@@ -107,7 +107,7 @@ static JavaRDD<Iterable<GATKRead>> groupReadsIntoPairs(final JavaRDD<GATKRead> p
         } else if (unpairedReads != null) {
             groupedReads = unpairedReads.map(Collections::singletonList);
         } else {
-            throw new UserException.BadInput("No reads were loaded. Ensure --pairedInput and/or --unpairedInput are set and valid.");
+            throw new UserException.BadInput("No reads were loaded. Ensure --paired-input and/or --unpaired-input are set and valid.");
         }
         return groupedReads;
     }

src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/PSUtils.java

@@ -67,7 +67,7 @@ public static int pathseqGetRecommendedNumReducers(final String inputPath, final
 
     /**
      * Returns a deep copy of the input header with an empty sequence dictionary, and logs warnings if the input may
-     * be aligned but --isHostAligned was not set to true (or vice versa).
+     * be aligned but --is-host-aligned was not set to true (or vice versa).
      */
     public static SAMFileHeader checkAndClearHeaderSequences(final SAMFileHeader inputHeader, final PSFilterArgumentCollection filterArgs, final Logger logger) {
 
@@ -79,10 +79,10 @@ public static SAMFileHeader checkAndClearHeaderSequences(final SAMFileHeader inp
         final SAMFileHeader header = inputHeader.clone();
 
         if (filterArgs.alignedInput && (header.getSequenceDictionary() == null || header.getSequenceDictionary().isEmpty())) {
-            logger.warn("--isHostAligned is true but the BAM header contains no sequences");
+            logger.warn("--is-host-aligned is true but the BAM header contains no sequences");
         }
         if (!filterArgs.alignedInput && header.getSequenceDictionary() != null && !header.getSequenceDictionary().isEmpty()) {
-            logger.warn("--isHostAligned is false but there are one or more sequences in the BAM header");
+            logger.warn("--is-host-aligned is false but there are one or more sequences in the BAM header");
         }
 
         //Clear header sequences

src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBuildReferenceTaxonomy.java

@@ -122,7 +122,7 @@ public class PathSeqBuildReferenceTaxonomy extends CommandLineProgram {
     public Object doWork() {
 
         if (refseqCatalogPath == null && genbankCatalogPath == null) {
-            throw new UserException.BadInput("At least one of --refseqCatalogPath or --genbankCatalogPath must be specified");
+            throw new UserException.BadInput("At least one of --refseq-catalog or --genbank-catalog must be specified");
         }
 
         logger.info("Parsing reference and files... (this may take a few minutes)");

src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqBwaSpark.java

@@ -212,15 +212,15 @@ private boolean alignBam(final String inputBamPath, final PSBwaAlignerSpark alig
     protected void runTool(final JavaSparkContext ctx) {
 
         if (!readArguments.getReadFiles().isEmpty()) {
-            throw new UserException.BadInput("Please use --pairedInput or --unpairedInput instead of --input");
+            throw new UserException.BadInput("Please use --paired-input or --unpaired-input instead of --input");
         }
         final ReadsSparkSource readsSource = new ReadsSparkSource(ctx, readArguments.getReadValidationStringency());
 
         final PSBwaAlignerSpark aligner = new PSBwaAlignerSpark(ctx, bwaArgs);
         boolean bPairedSuccess = alignBam(inputPaired, aligner, true, ctx, readsSource);
         boolean bUnpairedSuccess = alignBam(inputUnpaired, aligner, false, ctx, readsSource);
         if (!bPairedSuccess && !bUnpairedSuccess) {
-            throw new UserException.BadInput("No reads were loaded. Ensure --pairedInput and/or --unpairedInput are set and valid.");
+            throw new UserException.BadInput("No reads were loaded. Ensure --paired-input and/or --unpaired-input are set and valid.");
         }
         aligner.close();
     }

src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqPipelineSpark.java

@@ -93,7 +93,7 @@
  * <h4>Local mode:</h4>
  *
  * <pre>
- * gatk PathSeqFilterSpark  \
+ * gatk PathSeqPipelineSpark  \
  *   --input input_reads.bam \
  *   --kmer-file host_kmers.bfi \
  *   --filter-bwa-image host_reference.img \
@@ -112,7 +112,7 @@
  * <h4>Spark cluster on Google Cloud DataProc with 6 16-core / 208GB memory worker nodes:</h4>
  *
  * <pre>
- * gatk PathSeqFilterSpark  \
+ * gatk PathSeqPipelineSpark  \
  *   --input gs://my-gcs-bucket/input_reads.bam \
  *   --kmer-file hdfs://my-cluster-m:8020//host_kmers.bfi \
  *   --filter-bwa-image /references/host_reference.img \

src/main/java/org/broadinstitute/hellbender/tools/spark/pathseq/PathSeqScoreSpark.java

@@ -186,7 +186,7 @@ static SAMFileHeader joinBamHeaders(final SAMFileHeader pairedHeader, final SAMF
     protected void runTool(final JavaSparkContext ctx) {
 
         if (!readArguments.getReadFiles().isEmpty()) {
-            throw new UserException.BadInput("Please use --pairedInput or --unpairedInput instead of --input");
+            throw new UserException.BadInput("Please use --paired-input or --unpaired-input instead of --input");
         }
 
         final ReadsSparkSource readsSource = new ReadsSparkSource(ctx, readArguments.getReadValidationStringency());

src/main/java/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs.java

@@ -93,7 +93,7 @@ public final class CombineGVCFs extends MultiVariantWalkerGroupedOnStart {
      * span across a given genomic position (e.g. when scatter-gathering jobs across a compute farm).  The option below enables users to break bands at
      * pre-defined positions.  For example, a value of 10,000 would mean that we would ensure that no bands span across chr1:10000, chr1:20000, etc.
      *
-     * Note that the --convertToBasePairResolution argument is just a special case of this argument with a value of 1.
+     * Note that the --convert-to-base-pair-resolution argument is just a special case of this argument with a value of 1.
      */
     @Argument(fullName=BREAK_BANDS_LONG_NAME, doc = "If > 0, reference bands will be broken up at genomic positions that are multiples of this number", optional=true)
     protected int multipleAtWhichToBreakBands = 0;

src/main/java/org/broadinstitute/hellbender/tools/walkers/filters/VariantFiltration.java

@@ -87,9 +87,9 @@ public final class VariantFiltration extends VariantWalker {
 
     /**
      * Any variant which overlaps entries from the provided mask file will be filtered. If the user wants logic to be reversed,
-     * i.e. filter variants that do not overlap with provided mask, then argument -filterNotInMask can be used.
+     * i.e. filter variants that do not overlap with provided mask, then argument --filter-not-in-mask can be used.
      * Note that it is up to the user to adapt the name of the mask to make it clear that the reverse logic was used
-     * (e.g. if masking against Hapmap, use -maskName=hapmap for the normal masking and -maskName=not_hapmap for the reverse masking).
+     * (e.g. if masking against Hapmap, use --mask-name=hapmap for the normal masking and --mask-name=not_hapmap for the reverse masking).
      */
     @Argument(fullName="mask", shortName="mask", doc="Input mask", optional=true)
     public FeatureInput<Feature> mask;
@@ -142,20 +142,20 @@ public final class VariantFiltration extends VariantWalker {
     public Integer maskExtension = 0;
 
     /**
-     * When using the -mask argument, the maskName will be annotated in the variant record.
-     * Note that when using the -filter-not-in-mask argument to reverse the masking logic,
+     * When using the --mask argument, the mask-name will be annotated in the variant record.
+     * Note that when using the --filter-not-in-mask argument to reverse the masking logic,
      * it is up to the user to adapt the name of the mask to make it clear that the reverse logic was used
-     * (e.g. if masking against Hapmap, use -mask-name=hapmap for the normal masking and -mask-name=not_hapmap for the reverse masking).
+     * (e.g. if masking against Hapmap, use --mask-name=hapmap for the normal masking and --mask-name=not_hapmap for the reverse masking).
      */
     @Argument(fullName=MASK_NAME_LONG_NAME, doc="The text to put in the FILTER field if a 'mask' is provided and overlaps with a variant call", optional=true)
     public String maskName = "Mask";
 
     /**
-     * By default, if the -mask argument is used, any variant falling in a mask will be filtered.
+     * By default, if the --mask argument is used, any variant falling in a mask will be filtered.
      * If this argument is used, logic is reversed, and variants falling outside a given mask will be filtered.
      * Use case is, for example, if we have an interval list or BED file with "good" sites.
      * Note that it is up to the user to adapt the name of the mask to make it clear that the reverse logic was used
-     * (e.g. if masking against Hapmap, use -mask-name=hapmap for the normal masking and -mask-name=not_hapmap for the reverse masking).
+     * (e.g. if masking against Hapmap, use --mask-name=hapmap for the normal masking and --mask-name=not_hapmap for the reverse masking).
      */
     @Argument(fullName=FILTER_NOT_IN_MASK_LONG_NAME, doc="Filter records NOT in given input mask.", optional=true)
     public boolean filterRecordsNotInMask = false;
@@ -215,7 +215,7 @@ private static boolean invertLogic(final boolean logic, final boolean invert){
     }
 
     /**
-     * Prepend inverse phrase to description if --invertFilterExpression
+     * Prepend inverse phrase to description if --invert-filter-expression
      *
      * @param description the description
      * @return the description with inverse prepended if --invert_filter_expression

src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeCalculationArgumentCollection.java

@@ -162,7 +162,7 @@ public GenotypeCalculationArgumentCollection( final GenotypeCalculationArgumentC
      * f) If user-defined values add to more than one, an error will be produced.
      *
      * If user wants completely flat priors, then user should specify the same value (=1/(2*N+1)) 2*N times,e.g.
-     *   -inputPrior 0.33 -inputPrior 0.33
+     *   --input-prior 0.33 --input-prior 0.33
      * for the single-sample diploid case.
      */
     @Advanced

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerArgumentCollection.java

@@ -103,7 +103,7 @@ public class HaplotypeCallerArgumentCollection extends AssemblyBasedCallerArgume
      * If set, certain "early exit" optimizations in HaplotypeCaller, which aim to save compute and time by skipping
      * calculations if an ActiveRegion is determined to contain no variants, will be disabled. This is most likely to be useful if
      * you're using the -bamout argument to examine the placement of reads following reassembly and are interested in seeing the mapping of
-     * reads in regions with no variations. Setting the -forceActive and -dontTrimActiveRegions flags may also be necessary.
+     * reads in regions with no variations. Setting the --force-active and --dont-trim-active-regions flags may also be necessary.
      */
     @Advanced
     @Argument(fullName = "disable-optimizations", doc="Don't skip calculations in ActiveRegions with no variants",

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/HaplotypeCallerEngine.java

@@ -268,7 +268,7 @@ private void validateAndInitializeArgs() {
         Utils.validateArg(hcArgs.likelihoodArgs.BASE_QUALITY_SCORE_THRESHOLD >= QualityUtils.MIN_USABLE_Q_SCORE, "BASE_QUALITY_SCORE_THRESHOLD must be greater than or equal to " + QualityUtils.MIN_USABLE_Q_SCORE + " (QualityUtils.MIN_USABLE_Q_SCORE)");
 
         if ( emitReferenceConfidence() && samplesList.numberOfSamples() != 1 ) {
-            throw new CommandLineException.BadArgumentValue("--emitRefConfidence", "Can only be used in single sample mode currently. Use the sample_name argument to run on a single sample out of a multi-sample BAM file.");
+            throw new CommandLineException.BadArgumentValue("--emit-ref-confidence", "Can only be used in single sample mode currently. Use the --sample-name argument to run on a single sample out of a multi-sample BAM file.");
         }
     }
 

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/ReadThreadingAssemblerArgumentCollection.java

@@ -19,7 +19,7 @@ public final class ReadThreadingAssemblerArgumentCollection implements Serializa
     // -----------------------------------------------------------------------------------------------
 
     /**
-     * Multiple kmer sizes can be specified, using e.g. `-kmerSize 10 -kmerSize 25`.
+     * Multiple kmer sizes can be specified, using e.g. `--kmer-size 10 --kmer-size 25`.
      */
     @Advanced
     @Argument(fullName="kmer-size", doc="Kmer size to use in the read threading assembler", optional = true)

src/main/java/org/broadinstitute/hellbender/tools/walkers/validation/AnnotateVcfWithExpectedAlleleFraction.java

@@ -43,7 +43,7 @@
  * gatk --java-options "-Xmx4g" AnnotateVcfWithExpectedAlleleFraction \
  *   -V input.vcf \
  *   -O output.vcf \
- *   -mixingFractions mixingFractions.table
+ *   --mixing-fractions mixingFractions.table
  * </pre>
  *
  * Created by David Benjamin on 1/31/17.

src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/CalculateGenotypePosteriors.java

@@ -75,8 +75,8 @@
  * By default, priors will be applied to each variant separately, provided each variant features data from at least
  * 10 called samples (no-calls do not count). SNP sites in the input callset that have a SNP at the matching site in
  * the supporting VCF will have priors applied based on the AC from the supporting samples and the input callset
- * unless the --ignoreInputSamples flag is used. If a site is not called in the supporting VCF, priors will be
- * applied using the discovered AC from the input samples unless the --discoveredACpriorsOff flag is used.
+ * unless the --ignore-input-samples flag is used. If a site is not called in the supporting VCF, priors will be
+ * applied using the discovered AC from the input samples unless the --discovered-allele-count-priors-off flag is used.
  * For any non-SNP sites in the input callset, flat priors are applied.
  * </p>
  *
@@ -103,7 +103,7 @@
  *   -V input.vcf.gz \
  *   -O output.vcf.gz \
  *   -ped family.ped \
- *   --skipPopulationPriors
+ *   --skip-population-priors
  * </pre>
  *
  * <h4>Apply frequency and HWE-based priors to the genotypes of a family without including the family allele counts
@@ -112,7 +112,7 @@
  * gatk --java-options "-Xmx4g" CalculateGenotypePosteriors \
  *   -V input.vcf.gz \
  *   -O output.vcf.gz \
- *   --ignoreInputSamples
+ *   --ignore-input-samples
  * </pre>
  *
  * <h4>Calculate the posterior genotypes of a callset, and impose that a variant *not seen* in the external panel

src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/ApplyVQSR.java

@@ -171,7 +171,7 @@ public class ApplyVQSR extends MultiVariantWalker {
     protected Double VQSLOD_CUTOFF = null;
 
     /**
-     * For this to work properly, the -ignoreFilter argument should also be applied to the VariantRecalibration command.
+     * For this to work properly, the --ignore-filter argument should also be applied to the VariantRecalibration command.
      */
     @Argument(fullName="ignore-filter", doc="If specified, the recalibration will be applied to variants marked as filtered by the specified filter name in the input VCF file", optional=true)
     private List<String> IGNORE_INPUT_FILTERS = new ArrayList<>();
@@ -246,7 +246,7 @@ public void onTraversalStart() {
         if( TS_FILTER_LEVEL != null ) {
             // if the user specifies both ts_filter_level and lodCutoff then throw a user error
             if( VQSLOD_CUTOFF != null ) {
-                throw new UserException("Arguments --ts_filter_level and --lodCutoff are mutually exclusive. Please only specify one option.");
+                throw new UserException("Arguments --truth-sensitivity-filter-level and --lod-score-cutoff are mutually exclusive. Please only specify one option.");
             }
 
             if( tranches.size() >= 2 ) {

src/main/java/org/broadinstitute/hellbender/tools/walkers/vqsr/CNNVariantTrain.java

@@ -21,7 +21,7 @@
  * <h3>Inputs</h3>
  * <ul>
  *      <li>data-dir The training data created by {@link CNNVariantWriteTensors}.</li>
- *      <li>The tensor-name argument determines what types of tensors the model will expect.
+ *      <li>The --tensor-type argument determines what types of tensors the model will expect.
  *      Set it to "reference" for 1D tensors or "read_tensor" for 2D tensors.</li>
  * </ul>
  *
@@ -37,17 +37,17 @@
  * <h4>Train a 1D CNN on Reference Tensors</h4>
  * <pre>
  * gatk CNNVariantTrain \
- *   -tensor-type reference \
- *   -input-tensors-dir my_tensor_folder \
- *   -model-name my_1d_model
+ *   --tensor-type reference \
+ *   --input-tensor-dir my_tensor_folder \
+ *   --model-name my_1d_model
  * </pre>
  *
  * <h4>Train a 2D CNN on Read Tensors</h4>
  * <pre>
  * gatk CNNVariantTrain \
- *   -input-tensors-dir my_tensor_folder \
- *   -tensor-type read-tensor \
- *   -model-name my_2d_model
+ *   --input-tensor-dir my_tensor_folder \
+ *   --tensor-type read-tensor \
+ *   --model-name my_2d_model
  * </pre>
  *
  */