File Coverage

bin/bioaln

Criterion	Covered	Total	%
statement	37	37	100.0
branch	2	4	50.0
condition			n/a
subroutine	11	11	100.0
pod			n/a
total	50	52	96.1

#!/usr/bin/env perl

use strict;
use warnings;

use v5.10;
use Getopt::Long qw( :config bundling permute no_getopt_compat );
use Pod::Usage;
use Path::Tiny;
use lib path($0)->absolute->parent->sibling('lib')->stringify;

use Pod::Usage;
use Bio::BPWrapper;
use Bio::BPWrapper::AlnManipulations;

################################################################################
# Option parsing
################################################################################
my %opts;
GetOptions(
    \%opts,
    "help|h",
    "man",
    "version|V",
    "aln-index|I=s",
    "avg-pid|a",
    "binary", # 0/1 for binary sites (for phylip legacy programs)
    "bin-inform", # extract binary & informative sites (for clique): discard constant, 3/4-states, non-informative
    "bin-ref=s",
    "boot|b",
    "codon-view|c:20",    # Optional value, default 20
    "con-blocks|B:6",
    "concat|A",
    "consensus|C:50",
    "delete|d=s",
    "dna2pep|D",
    "gap-char=s",
    "gap-states",
    "gap-states2",
    "input|i=s",
    "length|l",
    "list-ids|L",
    "match|m",
    "no-flat|F",
    "no-gaps|g",
    "num-seq|n",
    "output|o=s",
    "pair-diff", # pairwise sequence diff
    "pair-diff-ref=s", # pairwise sequence diff to a ref seq
    "pep2dna|P=s",
    "permute-states|M",
    "phy-nonint", # non-interleaved phylip (for e.g.,clique)
    "pick|p=s",
    "random-slice=i",
    "ref-seq|r=s",
    "remove-third",
    "resample|R:i",    # Optional value, default is floor of num_sequences/2
    "rm-col|E=s",
    "select-third",
    "shuffle-sites|S",
    "slice|s=s",
    "split-cdhit=s",
    "trim-ends",
    "uniq|u",
    "upper", # make upper case (for DNAStatistics)
    "var-sites|v",
    "window|w:30",
  #  "dnadist|D=s", # Needs fixing
  #  "inform|Z",
) or pod2usage(2);

use constant PROGRAM => File::Basename::basename(__FILE__);
Bio::BPWrapper::print_version(PROGRAM) if $opts{"version"};

initialize(\%opts);
write_out(\%opts);

################# POD Documentation ############

__END__