2 #define MY_VERSION "4.2"
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11 STR_OPT( clstr2uc, 0)
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12 STR_OPT( uc2clstr, 0)
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13 STR_OPT( uc2fasta, 0)
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14 STR_OPT( uc2fastax, 0)
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15 STR_OPT( mergesort, 0)
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16 STR_OPT( tmpdir, ".")
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17 STR_OPT( staralign, 0)
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19 STR_OPT( blastout, 0)
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20 STR_OPT( blast6out, 0)
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21 STR_OPT( fastapairs, 0)
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22 STR_OPT( idchar, "|")
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23 STR_OPT( diffchar, " ")
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25 STR_OPT( gapopen, 0)
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28 STR_OPT( ids, "99,98,95,90,85,80,70,50,35")
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31 STR_OPT( clumpout, 0)
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32 STR_OPT( clump2fasta, 0)
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33 STR_OPT( clumpfasta, 0)
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34 STR_OPT( hireout, 0)
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35 STR_OPT( mergeclumps, 0)
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37 STR_OPT( hspalpha, 0)
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40 STR_OPT( tracestate, 0)
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41 STR_OPT( chainout, 0)
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42 STR_OPT( cluster, 0)
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43 STR_OPT( computekl, 0)
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44 STR_OPT( userout, 0)
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45 STR_OPT( userfields, 0)
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46 STR_OPT( seedsout, 0)
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47 STR_OPT( chainhits, 0)
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48 STR_OPT( findorfs, 0)
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50 STR_OPT( getseqs, 0)
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53 STR_OPT( makeindex, 0)
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54 STR_OPT( indexstats, 0)
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55 STR_OPT( uchimeout, 0)
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56 STR_OPT( uchimealns, 0)
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58 STR_OPT( mkctest, 0)
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59 STR_OPT( allpairs, 0)
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60 STR_OPT( fastq2fasta, 0)
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61 STR_OPT( otusort, 0)
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62 STR_OPT( sparsedist, 0)
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63 STR_OPT( sparsedistparams, 0)
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71 UNS_OPT( band, 16, 0, UINT_MAX)
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72 UNS_OPT( minlen, 10, 1, UINT_MAX)
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73 UNS_OPT( maxlen, 10000, 1, UINT_MAX)
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74 UNS_OPT( w, 0, 1, UINT_MAX)
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75 UNS_OPT( k, 0, 1, UINT_MAX)
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76 UNS_OPT( stepwords, 8, 0, UINT_MAX)
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77 UNS_OPT( maxaccepts, 1, 0, UINT_MAX)
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78 UNS_OPT( maxrejects, 8, 0, UINT_MAX)
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79 UNS_OPT( maxtargets, 0, 0, UINT_MAX)
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80 UNS_OPT( minhsp, 32, 1, UINT_MAX)
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81 UNS_OPT( bump, 50, 0, 100)
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82 UNS_OPT( rowlen, 64, 8, UINT_MAX)
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83 UNS_OPT( idprefix, 0, 0, UINT_MAX)
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84 UNS_OPT( idsuffix, 0, 0, UINT_MAX)
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85 UNS_OPT( chunks, 4, 2, UINT_MAX)
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86 UNS_OPT( minchunk, 64, 2, UINT_MAX)
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87 UNS_OPT( maxclump, 1000, 1, UINT_MAX)
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88 UNS_OPT( iddef, 0, 0, UINT_MAX)
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89 UNS_OPT( mincodons, 20, 1, UINT_MAX)
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90 UNS_OPT( maxovd, 8, 0, UINT_MAX)
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91 UNS_OPT( max2, 40, 0, UINT_MAX)
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92 UNS_OPT( querylen, 500, 0, UINT_MAX)
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93 UNS_OPT( targetlen, 500, 0, UINT_MAX)
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94 UNS_OPT( orfstyle, (1+2+4), 0, UINT_MAX)
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95 UNS_OPT( dbstep, 1, 1, UINT_MAX)
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96 UNS_OPT( randseed, 1, 0, UINT_MAX)
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97 UNS_OPT( maxp, 2, 2, UINT_MAX)
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98 UNS_OPT( idsmoothwindow, 32, 1, UINT_MAX)
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99 UNS_OPT( mindiffs, 3, 1, UINT_MAX)
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100 UNS_OPT( maxspan1, 24, 1, UINT_MAX)
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101 UNS_OPT( maxspan2, 24, 1, UINT_MAX)
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102 UNS_OPT( minorfcov, 16, 1, UINT_MAX)
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103 UNS_OPT( hashsize, 4195879, 1, UINT_MAX)
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104 UNS_OPT( maxpoly, 0, 0, UINT_MAX)
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105 UNS_OPT( droppct, 50, 0, 100)
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106 UNS_OPT( secs, 10, 0, UINT_MAX)
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107 UNS_OPT( maxqgap, 0, 0, UINT_MAX)
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108 UNS_OPT( maxtgap, 0, 0, UINT_MAX)
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110 INT_OPT( frame, 0, -3, +3)
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112 TOG_OPT( trace, false)
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113 TOG_OPT( logmemgrows, false)
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114 TOG_OPT( trunclabels, false)
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115 TOG_OPT( verbose, false)
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116 TOG_OPT( wordcountreject, true)
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117 TOG_OPT( rev, false)
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118 TOG_OPT( output_rejects, false)
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119 TOG_OPT( blast_termgaps, false)
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120 TOG_OPT( fastalign, true)
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121 TOG_OPT( flushuc, false)
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122 TOG_OPT( stable_sort, false)
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123 TOG_OPT( minus_frames, true)
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124 TOG_OPT( usort, true)
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125 TOG_OPT( nb, false)
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126 TOG_OPT( twohit, true)
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127 TOG_OPT( ssort, false)
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128 TOG_OPT( log_query, false)
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129 TOG_OPT( log_hothits, false)
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130 TOG_OPT( logwordstats, false)
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131 TOG_OPT( ucl, false)
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132 TOG_OPT( skipgaps2, true)
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133 TOG_OPT( skipgaps, true)
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134 TOG_OPT( denovo, false)
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135 TOG_OPT( cartoon_orfs, false)
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136 TOG_OPT( label_ab, false)
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137 TOG_OPT( wordweight, false)
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138 TOG_OPT( isort, false)
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139 TOG_OPT( selfid, false)
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140 TOG_OPT( leftjust, false)
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141 TOG_OPT( rightjust, false)
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143 FLT_OPT( id, 0.0, 0.0, 1.0)
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144 FLT_OPT( weak_id, 0.0, 0.0, 1.0)
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145 FLT_OPT( match, 1.0, 0.0, FLT_MAX)
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146 FLT_OPT( mismatch, -2.0, 0.0, FLT_MAX)
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147 FLT_OPT( split, 1000.0, 1.0, FLT_MAX)
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148 FLT_OPT( evalue, 10.0, 0.0, FLT_MAX)
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149 FLT_OPT( weak_evalue, 10.0, 0.0, FLT_MAX)
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150 FLT_OPT( evalue_g, 10.0, 0.0, FLT_MAX)
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151 FLT_OPT( chain_evalue, 10.0, 0.0, FLT_MAX)
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152 FLT_OPT( xdrop_u, 16.0, 0.0, FLT_MAX)
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153 FLT_OPT( xdrop_g, 32.0, 0.0, FLT_MAX)
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154 FLT_OPT( xdrop_ug, 16.0, 0.0, FLT_MAX)
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155 FLT_OPT( xdrop_nw, 16.0, 0.0, FLT_MAX)
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156 FLT_OPT( ka_gapped_lambda, 0.0, 0.0, FLT_MAX)
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157 FLT_OPT( ka_ungapped_lambda, 0.0, 0.0, FLT_MAX)
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158 FLT_OPT( ka_gapped_k, 0.0, 0.0, FLT_MAX)
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159 FLT_OPT( ka_ungapped_k, 0.0, 0.0, FLT_MAX)
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160 FLT_OPT( ka_dbsize, 0.0, 0.0, FLT_MAX)
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161 FLT_OPT( chain_targetfract, 0.0, 0.0, 1.0)
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162 FLT_OPT( targetfract, 0.0, 0.0, 1.0)
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163 FLT_OPT( queryfract, 0.0, 0.0, 1.0)
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164 FLT_OPT( fspenalty, 16.0, 0.0, FLT_MAX)
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165 FLT_OPT( sspenalty, 20.0, 0.0, FLT_MAX)
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166 FLT_OPT( seedt1, 13.0, 0.0, FLT_MAX)
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167 FLT_OPT( seedt2, 11.0, 0.0, FLT_MAX)
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168 FLT_OPT( lopen, 11.0, 0.0, FLT_MAX)
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169 FLT_OPT( lext, 1.0, 0.0, FLT_MAX)
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170 FLT_OPT( minh, 0.3, 0.0, FLT_MAX)
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171 FLT_OPT( xn, 8.0, 0.0, FLT_MAX)
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172 FLT_OPT( dn, 1.4, 0.0, FLT_MAX)
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173 FLT_OPT( xa, 1.0, 0.0, FLT_MAX)
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174 FLT_OPT( mindiv, 0.5, 0.0, 100.0)
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175 FLT_OPT( abskew, 2, 0.0, 100.0)
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176 FLT_OPT( abx, 8.0, 0.0, 100.0)
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177 FLT_OPT( minspanratio1, 0.7, 0.0, 1.0)
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178 FLT_OPT( minspanratio2, 0.7, 0.0, 1.0)
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180 FLAG_OPT( usersort)
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184 FLAG_OPT( ungapped)
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projects / mothur.git / blob