Update references to old-style arguments (#5063)

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

Author: keysmashes

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());