Merge pull request #798 from broadinstitute/rhl_rm_deprecated_classes…

…_510 Remove deprecated classes
broadinstitute · May 4, 2017 · da60c2b · da60c2b
2 parents e55e65a + 1a8ff34
commit da60c2b
Show file tree

Hide file tree

Showing 12 changed files with 4 additions and 2,368 deletions.
diff --git a/build.gradle b/build.gradle
@@ -149,15 +149,14 @@ tasks.withType(Test) {
 ext.htmlDir = new File("build/docs/html")
 ext.htmlDirInc = new File(htmlDir, "_includes")
 ext.commandClasses = ["picard.sam.AddCommentsToBam", "picard.sam.AddOrReplaceReadGroups", "picard.util.BaitDesigner", "picard.fastq.BamToBfq",
-                          "picard.sam.BamIndexStats", "picard.util.BedToIntervalList", "picard.sam.BuildBamIndex", "picard.analysis.directed.CalculateHsMetrics",
+                          "picard.sam.BamIndexStats", "picard.util.BedToIntervalList", "picard.sam.BuildBamIndex",
                           "picard.sam.CalculateReadGroupChecksum", "picard.sam.CleanSam", "picard.analysis.CollectAlignmentSummaryMetrics",
                           "picard.analysis.CollectBaseDistributionByCycle", "picard.analysis.CollectGcBiasMetrics", "picard.illumina.quality.CollectHiSeqXPfFailMetrics",
                           "picard.analysis.directed.CollectHsMetrics", "picard.illumina.CollectIlluminaBasecallingMetrics", "picard.illumina.CollectIlluminaLaneMetrics",
                           "picard.analysis.CollectInsertSizeMetrics", "picard.analysis.CollectJumpingLibraryMetrics", "picard.analysis.CollectMultipleMetrics",
                           "picard.analysis.CollectOxoGMetrics", "picard.analysis.CollectQualityYieldMetrics", "picard.analysis.CollectRawWgsMetrics",
                           "picard.analysis.directed.CollectTargetedPcrMetrics", "picard.analysis.CollectRnaSeqMetrics", "picard.analysis.CollectRrbsMetrics",
                           "picard.analysis.artifacts.CollectSequencingArtifactMetrics", "picard.vcf.CollectVariantCallingMetrics", "picard.analysis.CollectWgsMetrics",
-                          "picard.analysis.CollectWgsMetricsFromQuerySorted", "picard.analysis.CollectWgsMetricsFromSampledSites",
                           "picard.analysis.CollectWgsMetricsWithNonZeroCoverage", "picard.analysis.CompareMetrics", "picard.sam.CompareSAMs",
                           "picard.analysis.artifacts.ConvertSequencingArtifactToOxoG", "picard.sam.CreateSequenceDictionary", "picard.sam.DownsampleSam",
                           "picard.illumina.ExtractIlluminaBarcodes", "picard.sam.markduplicates.EstimateLibraryComplexity", "picard.sam.FastqToSam", "picard.util.FifoBuffer",

diff --git a/src/main/java/picard/analysis/CollectWgsMetrics.java b/src/main/java/picard/analysis/CollectWgsMetrics.java
@@ -126,8 +126,7 @@ public class CollectWgsMetrics extends CommandLineProgram {
 
     @Option(doc = "An interval list file that contains the positions to restrict the assessment. Please note that " +
             "all bases of reads that overlap these intervals will be considered, even if some of those bases extend beyond the boundaries of " +
-            "the interval. The ideal use case for this argument is to use it to restrict the calculation to a subset of (whole) contigs. To " +
-            "restrict the calculation just to individual positions without overlap, please see CollectWgsMetricsFromSampledSites.",
+            "the interval. The ideal use case for this argument is to use it to restrict the calculation to a subset of (whole) contigs.",
             optional = true, overridable = true)
     public File INTERVALS = null;
 

diff --git a/src/main/java/picard/analysis/CollectWgsMetricsFromQuerySorted.java b/src/main/java/picard/analysis/CollectWgsMetricsFromQuerySorted.java
diff --git a/src/main/java/picard/analysis/CollectWgsMetricsFromSampledSites.java b/src/main/java/picard/analysis/CollectWgsMetricsFromSampledSites.java
diff --git a/src/main/java/picard/analysis/directed/CalculateHsMetrics.java b/src/main/java/picard/analysis/directed/CalculateHsMetrics.java
diff --git a/src/main/java/picard/analysis/directed/CollectHsMetrics.java b/src/main/java/picard/analysis/directed/CollectHsMetrics.java
@@ -126,7 +126,7 @@ protected String getProbeSetName() {
 
     /** Stock main method. */
     public static void main(final String[] argv) {
-        System.exit(new CalculateHsMetrics().instanceMain(argv));
+        System.exit(new CollectHsMetrics().instanceMain(argv));
     }
 
     @Override