zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Added deprecation notice for SomaticIndelDetector

This commit is contained in:
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
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
public/java/src/org/broadinstitute/sting/utils/DeprecatedToolChecks.java
View File

@ -46,6 +46,7 @@ public class DeprecatedToolChecks {
deprecatedGATKWalkers.put("TableRecalibration", "2.0 (use PrintReads with -BQSR instead; see documentation for usage)");
deprecatedGATKWalkers.put("AlignmentWalker", "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