diff --git a/bin/cdhit_wrapper.R b/bin/cdhit_wrapper.R
index c9a8241..e5ed3e4 100644
--- a/bin/cdhit_wrapper.R
+++ b/bin/cdhit_wrapper.R
@@ -16,12 +16,12 @@ option_list <- list(
   # make_option(opt_str = c("-d", "--description")), # can not produce bed if this is != 0
   make_option(opt_str = c("-s", "--length_dif_cutoff_shorter_p"), default = 0.0, help = "Shorter sequences length must be at least x percent of longer sequenecs length. Default = %default (CD-HIT parameter)", metavar = "double"),
   make_option(opt_str = c("-S", "--length_dif_cutoff_shorter_n"), default = 999999, help = "Length difference between sequences can not be higher than x nucleotides. Default = %default (CD-HIT parameter)", metavar = "integer"),
-  make_option(opt_str = c("-aL", "--alignment_coverage_longer_p"), default = 0.0, help = "Alignment must cover x percent of longer sequence. Default = %default (CD-HIT parameter)", metavar = "double"),
-  make_option(opt_str = c("-AL", "--alignment_coverage_longer_n"), default = 99999999, help = "There can not be more than x unaligned nucleotides on the longer sequence. Default = %default (CD-HIT parameter)", metavar = "integer"),
-  make_option(opt_str = c("-aS", "--alignment_coverage_shorter_p"), default = 0.0, help = "Alignment must cover x percent of shorter sequence. Default = %default (CD-HIT parameter)", metavar = "double"),
-  make_option(opt_str = c("-AS", "--alignment_coverage_shorter_n"), default = 99999999, help = "There can not be more than x unaligned nucleotides on the longer sequence. Default = %default (CD-HIT parameter)", metavar = "integer"),
-  make_option(opt_str = c("-uL", "--max_unmatched_longer_p"), default = 1.0, help = "Maximum unmatched percentage on longer sequence (excludes leading tailing gap). Default = %default (CD-HIT parameter)", metavar = "double"),
-  make_option(opt_str = c("-uS", "--max_unmatched_shorter_p"), default = 1.0, help = "Maximum unmatched percentage on shorter sequence (excludes leading tailing gap). Default = %default (CD-HIT parameter)", metavar = "double"),
+  make_option(opt_str = c("-e", "--alignment_coverage_longer_p"), default = 0.0, help = "Alignment must cover x percent of longer sequence. Default = %default (CD-HIT parameter: -aL)", metavar = "double"),
+  make_option(opt_str = c("-E", "--alignment_coverage_longer_n"), default = 99999999, help = "There can not be more than x unaligned nucleotides on the longer sequence. Default = %default (CD-HIT parameter: -AL)", metavar = "integer"),
+  make_option(opt_str = c("-f", "--alignment_coverage_shorter_p"), default = 0.0, help = "Alignment must cover x percent of shorter sequence. Default = %default (CD-HIT parameter: -aS)", metavar = "double"),
+  make_option(opt_str = c("-F", "--alignment_coverage_shorter_n"), default = 99999999, help = "There can not be more than x unaligned nucleotides on the longer sequence. Default = %default (CD-HIT parameter: -AS)", metavar = "integer"),
+  make_option(opt_str = c("-w", "--max_unmatched_longer_p"), default = 1.0, help = "Maximum unmatched percentage on longer sequence (excludes leading tailing gap). Default = %default (CD-HIT parameter: -uL)", metavar = "double"),
+  make_option(opt_str = c("-W", "--max_unmatched_shorter_p"), default = 1.0, help = "Maximum unmatched percentage on shorter sequence (excludes leading tailing gap). Default = %default (CD-HIT parameter: -uS)", metavar = "double"),
   make_option(opt_str = c("-U", "--max_unmatched_both_n"), default = 99999999, help = "Maximum unmatched nucleotied on both sequences (excludes leading tailing gap). Default = %default (CD-HIT parameter)", metavar = "integer"),
   make_option(opt_str = c("-g", "--fast_cluster"), default = 1, help = "Cluster sequence in first cluster that meets threshold = 0 (fast). Or cluster in best Cluster = 1 (accurate). Default = %default (CD-HIT parameter)", metavar = "integer"),
   make_option(opt_str = c("-r", "--strand"), default = 0, help = "Align +/+ & +/- (= 1). Or align only +/+ (= 0). Default = %default (CD-HIT parameter)", metavar = "integer"),
@@ -29,7 +29,7 @@ option_list <- list(
   make_option(opt_str = c("--mismatch"), default = -2, help = "Mismatch score. Default = %default (CD-HIT parameter)", metavar = "integer"),
   make_option(opt_str = c("--gap"), default = -6, help = "Gap score. Default = %default (CD-HIT parameter)", metavar = "integer"),
   make_option(opt_str = c("--gap_ext"), default = -1, help = "Gap extension score. Default = %default (CD-HIT parameter)", metavar = "integer"),
-  make_option(opt_str = c("-sc", "--sort_cluster_by_size"), default = 1, help = "Either sort cluster by decreasing length (= 0) or by decreasing size (= 1). Default = %default (CD-HIT parameter)", metavar = "integer")
+  make_option(opt_str = c("-x", "--sort_cluster_by_size"), default = 1, help = "Either sort cluster by decreasing length (= 0) or by decreasing size (= 1). Default = %default (CD-HIT parameter: -sc)", metavar = "integer")
 )
 
 opt_parser <- OptionParser(option_list = option_list,