added RepeatFiller and usage to the repo

yuzhenpeng · Jul 5, 2019 · 71afedf · 71afedf
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diff --git a/README.md b/README.md
@@ -48,7 +48,13 @@ RepeatFiller [5] is a tool to incorporate newly-detected repeat-overlapping alig
 
 __Usage:__
 ```
-coming soon
+RepeatFiller.py -c in.chain -T2 target.2bit -Q2 query.2bit [options]
+	in.chain	alignment file in chain format
+	target.2bit	full path to a .2bit file of reference species
+	query.2bit	full path to a .2bit file of query species
+	[options]	call RepeatFiller.py --help to see the full parameter list with description
+
+example: RepeatFiller.py -c hg38.speTri2.all.chain -T2 hg38.2bit -Q2 speTri2.2bit
 ```
 
 # Highly-sensitive local alignments