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Merge pull request #324 from broadinstitute/eb_AnalyzeCovariates_is_not_deprecated 

AnalyzeCovariates is no longer a deprecated tool.
This commit is contained in:
Eric Banks 2013-07-08 10:15:10 -07:00
parent bc28a1f236 921f551426
commit c5a2a8f39f
1 changed files with 0 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java
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@ -43,7 +43,6 @@ public class DeprecatedToolChecks {
static { static {
// Indicate recommended replacement in parentheses if applicable // Indicate recommended replacement in parentheses if applicable
deprecatedGATKWalkers.put("CountCovariates", "2.0 (use BaseRecalibrator instead; see documentation for usage)"); deprecatedGATKWalkers.put("CountCovariates", "2.0 (use BaseRecalibrator instead; see documentation for usage)");
deprecatedGATKWalkers.put("AnalyzeCovariates", "2.0 (use BaseRecalibrator instead; see documentation for usage)");
deprecatedGATKWalkers.put("TableRecalibration", "2.0 (use PrintReads with -BQSR instead; see documentation for usage)"); deprecatedGATKWalkers.put("TableRecalibration", "2.0 (use PrintReads with -BQSR instead; see documentation for usage)");
deprecatedGATKWalkers.put("AlignmentWalker", "2.2 (no replacement)"); deprecatedGATKWalkers.put("AlignmentWalker", "2.2 (no replacement)");
deprecatedGATKWalkers.put("CountBestAlignments", "2.2 (no replacement)"); deprecatedGATKWalkers.put("CountBestAlignments", "2.2 (no replacement)");