cmd.rb in cheripic-1.2.0

- old
+ new

@@ -38,10 +38,11 @@
     # trollop argument_parser for input args string and
     # @return [Hash] a hash of trollop option names as keys and user or default setting as values
     def argument_parser
       cmds = self
       Trollop::Parser.new do
+        version Cheripic::VERSION
         banner cmds.help_message
         opt :assembly, 'Assembly file in FASTA format',
             :short => '-f',
             :type => String
         opt :input_format, 'bulk and parent alignment file format types - set either pileup or bam',
@@ -74,13 +75,13 @@
             :type => Integer,
             :default => 3
         opt :min_indel_count_support, 'minimum read depth supporting an indel at each position',
             :type => Integer,
             :default => 3
-        opt :ignore_reference_n, 'ignore variant calls at N (completely ambigous) bases in the reference',
+        opt :ambiguous_ref_bases, 'including variant at completely ambiguous bases in the reference',
             :type => FalseClass,
-            :default => true
+            :default => false
         opt :mapping_quality, 'minimum mapping quality of read covering the position',
             :short => '-q',
             :type => Integer,
             :default => 20
         opt :base_quality, 'minimum base quality of bases covering the position',
@@ -91,16 +92,16 @@
             :type => Float,
             :default => 0.1
         opt :cross_type, 'type of cross used to generated mapping population - back or out',
             :type => String,
             :default => 'back'
-        opt :only_frag_with_vars, 'select only contigs containing variants for analysis',
+        opt :use_all_contigs, 'option to select all contigs or only contigs containing variants for analysis',
             :type => FalseClass,
-            :default => true
-        opt :filter_out_low_hmes, 'ignore variants from contigs with low hmescore or bfr to list in the final output',
+            :default => false
+        opt :include_low_hmes, 'option to include or discard variants from contigs with low hme-score or bfr score to list in the final output',
             :type => FalseClass,
-            :default => true
+            :default => false
         opt :polyploidy, 'Set if the data input is from polyploids',
             :type => FalseClass,
             :default => false
         opt :mut_parent, 'Pileup or sorted BAM file alignments from mutant/trait of interest parent',
             :short => '-p',
@@ -111,10 +112,13 @@
             :type => String,
             :default => ''
         opt :bfr_adjust, 'factor added to hemi snp frequency of each parent to adjust for bfr calculations',
             :type => Float,
             :default => 0.05
+        opt :sel_seq_len, 'sequence length to print from either side of selected variants',
+            :type => Integer,
+            :default => 50
         opt :examples, 'shows some example commands with explanation'
       end
     end
 
     # help message to display from command line
@@ -146,10 +150,15 @@
       msg = <<-EOS
 
         Cheripic v#{Cheripic::VERSION.dup}
 
         EXAMPLE COMMANDS:
-
+          1. cheripic -f assembly.fa -a mutbulk.pileup -b bgbulk.pileup --output=cheripic_output
+          2. cheripic --assembly assembly.fa --mut-bulk mutbulk.pileup --bg-bulk bgbulk.pileup
+                --mut-parent mutparent.pileup --bg-parent bgparent.pileup --polyploidy true --output cheripic_results
+          3. cheripic --assembly assembly.fa --mut-bulk mutbulk.pileup --bg-bulk bgbulk.pileup
+                --mut-parent mutparent.pileup --bg-parent bgparent.pileup --polyploidy true
+                --no-only-frag-with-vars --no-filter-out-low-hmes --output cheripic_results
       EOS
       puts msg.split("\n").map{ |line| line.lstrip }.join("\n")
       exit(0)
     end
 