Made keep_small_uniques the default in unique anchor filtering

MariaNattestad · May 26, 2016 · c1e7221 · c1e7221
1 parent d349c08
commit c1e7221
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/Assemblytics b/Assemblytics
@@ -54,7 +54,7 @@ echo "${OUTPUT_PREFIX##*/}"
 echo "STARTING,DONE,Starting unique anchor filtering."
 
 >&2 echo "1. Filter delta file"
-Assemblytics_uniq_anchor.py --delta $DELTA --unique-length $UNIQUE_LENGTH --out $OUTPUT_PREFIX
+Assemblytics_uniq_anchor.py --delta $DELTA --unique-length $UNIQUE_LENGTH --keep-small-uniques --out $OUTPUT_PREFIX
 if [ -e $OUTPUT_PREFIX.Assemblytics.unique_length_filtered_l$UNIQUE_LENGTH.delta.gz ];
 then
     echo "UNIQFILTER,DONE,Step 1: Assemblytics_uniq_anchor.py completed successfully. Now finding variants between alignments." 

diff --git a/Assemblytics_Nchart.R b/Assemblytics_Nchart.R
@@ -80,7 +80,7 @@ for (to_png in c(TRUE,FALSE)) {
                 geom_point(data=both.plot,size=2,alpha=0.5) + 
                 labs(x = paste("NG(x)% where 100% = ",bp_format(genome.length), sep=""),y="Sequence length",colour="Assembly",title="Cumulative sequence length") +
                 scale_color_manual(values=colors) +
-                annotation_logticks(sides="lr")
+                annotation_logticks(sides="lr",color="black")
               )
     } else {
         # To make bacterial genomes at least show a dot instead of an error because