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    index
    merge
    faidx
    pileup
    fixmate
    rmdup
    fillmd
);

# composite commands: pseudo-commands that run a
# sequence of commands
# composite command prefix => list of prefixes of commands this
#  composite command runs
#

# prefixes only for commands that take params/switches...
our %command_prefixes = (
    'view'       => 'view',
    'sort'       => 'srt',
    'index'      => 'idx',
    'merge'      => 'mrg',
    'faidx'      => 'fai',
    'pileup'     => 'pup',
    'fillmd'     => 'fmd'
    );

our @program_params = qw(
    command
    view|tab_delim
    view|out_file
    view|pass_flags
    view|filt_flags
    view|refseq
    view|qual_threshold
    view|library
    view|read_group
    srt|mem_hint
    mrg|headers_in
    pup|refseq
    pup|map_qcap
    pup|ref_list
    pup|site_list
    pup|theta
    pup|n_haplos
    pup|exp_hap_diff
    pup|indel_prob
    );

our @program_switches = qw(
    view|bam_output
    view|uncompressed
    view|add_header
    view|only_header
    view|sam_input
    srt|sort_by_names
    mrg|sort_by_names
    pup|qual_last_col
    pup|sam_input
    pup|indels_only
    pup|call_cons
    pup|genot_L
    fmd|match_with_eq
);

our %param_translation = (
    'view|tab_delim' => 't',
    'view|out_file' => 'o',
    'view|pass_flags' => 'f',
    'view|refseq'   => 'T',
    'view|filt_flags' => 'F',
    'view|qual_threshold' => 'q',
    'view|library' => 'l',
    'view|read_group' => 'r',
    'view|bam_output' => 'b',
    'view|uncompressed' => 'u',
    'view|add_header' => 'h',
    'view|only_header' => 'H',
    'view|sam_input' => 'S',
    'srt|mem_hint' => 'm',
    'srt|sort_by_names' => 'n',
    'mrg|headers_in' => 'h',
    'mrg|sort_by_names' => 'n',
    'pup|refseq' => 'f',
    'pup|map_qcap' => 'M',
    'pup|ref_list' => 't',
    'pup|site_list' => 'l',
    'pup|theta' => 'T',
    'pup|n_haplos' => 'N',
    'pup|exp_hap_diff' => 'f',
    'pup|indel_prob' => 'I',
    'pup|qual_last_col' => 's',
    'pup|sam_input' => 'S',
    'pup|indels_only' => 'i',
    'pup|call_cons' => 'c',
    'pup|genot_L' => 'g',
    'fmd|match_with_eq' => 'e'
    );

#
# the order in the arrayrefs is the order required
# on the command line
#
# the strings in the arrayrefs (less special chars)
# become the keys for named parameters to run_maq
#
# special chars:
#
# '#' implies optional
# '*' implies variable number of this type
# <|> implies stdin/stdout redirect
#

our %command_files = (
    'view' => [qw( bam #*rgn >out )],
    'sort' => [qw( bam >pfx )],
    'index' => [qw( bam )],
    'merge' => [qw( obm *ibm )],
    'faidx' => [qw( fas #*rgn )],
    'pileup' => [qw( bam >out )],
    'fixmate' => [qw( ibm obm )],
    'rmdup' => [qw( ibm obm )],
    'fillmd' => [qw( bam fas )]
    );

1;