Stat (#489)

* fix #307 by adding median and percentile

* add percentile parameter to change default value 90

* update doc to reflect add of percentile parameter

* add extra space between col1 and col2 to be sure to always separate these to column even if widht is set to low

* increase width of col1

bin/agat_sp_statistics.pl

@@ -14,6 +14,7 @@
 my $gff = undef;
 my $opt_output = undef;
 my $opt_yaml = undef;
+my $opt_percentile = 90;
 my $opt_genomeSize = undef;
 my $opt_plot = undef;
 my $opt_verbose = 0;
@@ -23,6 +24,7 @@
     'c|config=s'               => \$config,
     "h|help"      => \$opt_help,
     'o|output=s'  => \$opt_output,
+    'percentile=i' => \$opt_percentile,
     'yaml!'       => \$opt_yaml,
     'd|p'         => \$opt_plot,
     'v|verbose'   => \$opt_verbose,
@@ -102,6 +104,7 @@
 print "Compute statistics\n";
 print_omniscient_statistics ({ input   => $hash_omniscient,
 															 genome  => $opt_genomeSize,
+                               percentile => $opt_percentile,
 															 output  => $out,
                                yaml    => $opt_yaml,
 															 distri  => $opt_plot,
@@ -157,6 +160,10 @@ =head1 OPTIONS
 
 File where will be written the result. If no output file is specified, the output will be written to STDOUT.
 
+=item B<--percentile>
+
+Integer - Percentile to compute. Default is 90.
+
 =item B<--yaml>
 
 Bolean - When this option is activated , a second output will be printed either in STDOUT if no output provided or in <output.yaml> (a .yaml suffix is added to the --output value provided)

docs/tools/agat_sp_statistics.md

@@ -39,6 +39,10 @@ agat_sp_statistics.pl --help
 
     File where will be written the result. If no output file is specified, the output will be written to STDOUT.
 
+-  **--percentile**
+
+    Integer - Percentile to compute. Default is 90.
+
 - **--yaml**
 
     Bolean - When this option is activated , a second output will be printed either in STDOUT if no output provided or in <output.yaml> (a .yaml suffix is added to the --output value provided)