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Added deprecation notice for SomaticIndelDetector

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Geraldine Van der Auwera 2013-07-25 17:28:06 -04:00
parent 5ad99c362d
commit 660b075900
1 changed files with 1 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java
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@ -46,6 +46,7 @@ public class DeprecatedToolChecks {
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)");
deprecatedGATKWalkers.put("SomaticIndelDetector", "2.0 (replaced by the standalone tool Indelocator; see Cancer Tools documentation)");
} }
// Mapping from walker name to major version number where the walker first disappeared and optional replacement options // Mapping from walker name to major version number where the walker first disappeared and optional replacement options