while (<$file>) {
    if (my @captures = /
        (chr\d+:\d+-\d+)  #  0 Chromosome & coordinates
        \s+
        (numsnp=\d+)      #  1 Number of SNPs
        \s+
        (length=\S+)      #  2 CNV length (bp)
        \s+
        (state\d+)        #  3 HMM state
        ,
        (cn=\d+)          #  4 Copy number
        \s+
        (\S+)             #  5 File directory
        \/
        (\S+)             #  6 Sample I.D.
        \s+
        (startsnp=rs\d+)  #  7 First SNP in CNV
        \s+
        (endsnp=rs\d+)    #  8 Last SNP in CNV
        \s+
        (\S+)             #  9 Gene(s) overlapping CNV
        \s+
        (\S+)             # 10 Distance of gene(s) from CNV
    /x) {
        if ( $captures[1] >= 1 && $captures[1] <= 4 ) {
            ...
        } else {
            printf $out "%-28s %-30s %-12s %-10s %-18s %-22s %-21s %s\n",
                @matches[6,0,4,1,2,7,8,9];
        }
    }
}