Notes about adding more repeat masking

ktmeaton · Apr 22, 2020 · a4ce275 · a4ce275
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -9,6 +9,7 @@ and this project "attempts" to adhere to [Semantic Versioning](http://semver.org
 - Overabundance of files in database update and snippy_filtering
 - Deal with the fail to publish issue with NCBImeta db
 - Switch model testing from modeltest-ng to ModelFinder (because of the AVX/AVX2 requirement)
+- Add exact-repeats and tandem repeats detection
 
 ## [v0.1.1] - 2020-04-14
 

diff --git a/pipeline.nf b/pipeline.nf
@@ -458,6 +458,7 @@ if (!params.skip_reference_detect_repeats){
           {next;}
       else if (\$7 > 90)
           {print \$0}}' \${PREFIX}.inexact.coords > \${PREFIX}.inexact.repeats
+    # Also exact and tandem repeats??
     # Convert to bed file format, changing to 0-base position coordinates
     awk -F "\t" '{print \$12 "\t" \$1-1 "\t" \$2-1;
       if (\$3 > \$4){tmp=\$4; \$4=\$3; \$3=tmp;}