--- /dev/null
+#ifndef MY_VERSION\r
+#define MY_VERSION "4.2"\r
+#endif\r
+\r
+STR_OPT( input, 0)\r
+STR_OPT( query, 0)\r
+STR_OPT( db, 0)\r
+STR_OPT( sort, 0)\r
+STR_OPT( output, 0)\r
+STR_OPT( uc, 0)\r
+STR_OPT( clstr2uc, 0)\r
+STR_OPT( uc2clstr, 0)\r
+STR_OPT( uc2fasta, 0)\r
+STR_OPT( uc2fastax, 0)\r
+STR_OPT( mergesort, 0)\r
+STR_OPT( tmpdir, ".")\r
+STR_OPT( staralign, 0)\r
+STR_OPT( sortuc, 0)\r
+STR_OPT( blastout, 0)\r
+STR_OPT( blast6out, 0)\r
+STR_OPT( fastapairs, 0)\r
+STR_OPT( idchar, "|")\r
+STR_OPT( diffchar, " ")\r
+STR_OPT( uchime, 0)\r
+STR_OPT( gapopen, 0)\r
+STR_OPT( gapext, 0)\r
+STR_OPT( uhire, 0)\r
+STR_OPT( ids, "99,98,95,90,85,80,70,50,35")\r
+STR_OPT( seeds, 0)\r
+STR_OPT( clump, 0)\r
+STR_OPT( clumpout, 0)\r
+STR_OPT( clump2fasta, 0)\r
+STR_OPT( clumpfasta, 0)\r
+STR_OPT( hireout, 0)\r
+STR_OPT( mergeclumps, 0)\r
+STR_OPT( alpha, 0)\r
+STR_OPT( hspalpha, 0)\r
+STR_OPT( probmx, 0)\r
+STR_OPT( matrix, 0)\r
+STR_OPT( tracestate, 0)\r
+STR_OPT( chainout, 0)\r
+STR_OPT( cluster, 0)\r
+STR_OPT( computekl, 0)\r
+STR_OPT( userout, 0)\r
+STR_OPT( userfields, 0)\r
+STR_OPT( seedsout, 0)\r
+STR_OPT( chainhits, 0)\r
+STR_OPT( findorfs, 0)\r
+STR_OPT( strand, 0)\r
+STR_OPT( getseqs, 0)\r
+STR_OPT( labels, 0)\r
+STR_OPT( doug, 0)\r
+STR_OPT( makeindex, 0)\r
+STR_OPT( indexstats, 0)\r
+STR_OPT( uchimeout, 0)\r
+STR_OPT( uchimealns, 0)\r
+STR_OPT( xframe, 0)\r
+STR_OPT( mkctest, 0)\r
+STR_OPT( allpairs, 0)\r
+STR_OPT( fastq2fasta, 0)\r
+STR_OPT( otusort, 0)\r
+STR_OPT( sparsedist, 0)\r
+STR_OPT( sparsedistparams, 0)\r
+STR_OPT( mcc, 0)\r
+STR_OPT( utax, 0)\r
+STR_OPT( simcl, 0)\r
+STR_OPT( absort, 0)\r
+STR_OPT( cc, 0)\r
+STR_OPT( uslink, 0)\r
+\r
+UNS_OPT( band, 16, 0, UINT_MAX)\r
+UNS_OPT( minlen, 10, 1, UINT_MAX)\r
+UNS_OPT( maxlen, 10000, 1, UINT_MAX)\r
+UNS_OPT( w, 0, 1, UINT_MAX)\r
+UNS_OPT( k, 0, 1, UINT_MAX)\r
+UNS_OPT( stepwords, 8, 0, UINT_MAX)\r
+UNS_OPT( maxaccepts, 1, 0, UINT_MAX)\r
+UNS_OPT( maxrejects, 8, 0, UINT_MAX)\r
+UNS_OPT( maxtargets, 0, 0, UINT_MAX)\r
+UNS_OPT( minhsp, 32, 1, UINT_MAX)\r
+UNS_OPT( bump, 50, 0, 100)\r
+UNS_OPT( rowlen, 64, 8, UINT_MAX)\r
+UNS_OPT( idprefix, 0, 0, UINT_MAX)\r
+UNS_OPT( idsuffix, 0, 0, UINT_MAX)\r
+UNS_OPT( chunks, 4, 2, UINT_MAX)\r
+UNS_OPT( minchunk, 64, 2, UINT_MAX)\r
+UNS_OPT( maxclump, 1000, 1, UINT_MAX)\r
+UNS_OPT( iddef, 0, 0, UINT_MAX)\r
+UNS_OPT( mincodons, 20, 1, UINT_MAX)\r
+UNS_OPT( maxovd, 8, 0, UINT_MAX)\r
+UNS_OPT( max2, 40, 0, UINT_MAX)\r
+UNS_OPT( querylen, 500, 0, UINT_MAX)\r
+UNS_OPT( targetlen, 500, 0, UINT_MAX)\r
+UNS_OPT( orfstyle, (1+2+4), 0, UINT_MAX)\r
+UNS_OPT( dbstep, 1, 1, UINT_MAX)\r
+UNS_OPT( randseed, 1, 0, UINT_MAX)\r
+UNS_OPT( maxp, 2, 2, UINT_MAX)\r
+UNS_OPT( idsmoothwindow, 32, 1, UINT_MAX)\r
+UNS_OPT( mindiffs, 3, 1, UINT_MAX)\r
+UNS_OPT( maxspan1, 24, 1, UINT_MAX)\r
+UNS_OPT( maxspan2, 24, 1, UINT_MAX)\r
+UNS_OPT( minorfcov, 16, 1, UINT_MAX)\r
+UNS_OPT( hashsize, 4195879, 1, UINT_MAX)\r
+UNS_OPT( maxpoly, 0, 0, UINT_MAX)\r
+UNS_OPT( droppct, 50, 0, 100)\r
+UNS_OPT( secs, 10, 0, UINT_MAX)\r
+UNS_OPT( maxqgap, 0, 0, UINT_MAX)\r
+UNS_OPT( maxtgap, 0, 0, UINT_MAX)\r
+\r
+INT_OPT( frame, 0, -3, +3)\r
+\r
+TOG_OPT( trace, false)\r
+TOG_OPT( logmemgrows, false)\r
+TOG_OPT( trunclabels, false)\r
+TOG_OPT( verbose, false)\r
+TOG_OPT( wordcountreject, true)\r
+TOG_OPT( rev, false)\r
+TOG_OPT( output_rejects, false)\r
+TOG_OPT( blast_termgaps, false)\r
+TOG_OPT( fastalign, true)\r
+TOG_OPT( flushuc, false)\r
+TOG_OPT( stable_sort, false)\r
+TOG_OPT( minus_frames, true)\r
+TOG_OPT( usort, true)\r
+TOG_OPT( nb, false)\r
+TOG_OPT( twohit, true)\r
+TOG_OPT( ssort, false)\r
+TOG_OPT( log_query, false)\r
+TOG_OPT( log_hothits, false)\r
+TOG_OPT( logwordstats, false)\r
+TOG_OPT( ucl, false)\r
+TOG_OPT( skipgaps2, true)\r
+TOG_OPT( skipgaps, true)\r
+TOG_OPT( denovo, false)\r
+TOG_OPT( cartoon_orfs, false)\r
+TOG_OPT( label_ab, false)\r
+TOG_OPT( wordweight, false)\r
+TOG_OPT( isort, false)\r
+TOG_OPT( selfid, false)\r
+TOG_OPT( leftjust, false)\r
+TOG_OPT( rightjust, false)\r
+\r
+FLT_OPT( id, 0.0, 0.0, 1.0)\r
+FLT_OPT( weak_id, 0.0, 0.0, 1.0)\r
+FLT_OPT( match, 1.0, 0.0, FLT_MAX)\r
+FLT_OPT( mismatch, -2.0, 0.0, FLT_MAX)\r
+FLT_OPT( split, 1000.0, 1.0, FLT_MAX)\r
+FLT_OPT( evalue, 10.0, 0.0, FLT_MAX)\r
+FLT_OPT( weak_evalue, 10.0, 0.0, FLT_MAX)\r
+FLT_OPT( evalue_g, 10.0, 0.0, FLT_MAX)\r
+FLT_OPT( chain_evalue, 10.0, 0.0, FLT_MAX)\r
+FLT_OPT( xdrop_u, 16.0, 0.0, FLT_MAX)\r
+FLT_OPT( xdrop_g, 32.0, 0.0, FLT_MAX)\r
+FLT_OPT( xdrop_ug, 16.0, 0.0, FLT_MAX)\r
+FLT_OPT( xdrop_nw, 16.0, 0.0, FLT_MAX)\r
+FLT_OPT( ka_gapped_lambda, 0.0, 0.0, FLT_MAX)\r
+FLT_OPT( ka_ungapped_lambda, 0.0, 0.0, FLT_MAX)\r
+FLT_OPT( ka_gapped_k, 0.0, 0.0, FLT_MAX)\r
+FLT_OPT( ka_ungapped_k, 0.0, 0.0, FLT_MAX)\r
+FLT_OPT( ka_dbsize, 0.0, 0.0, FLT_MAX)\r
+FLT_OPT( chain_targetfract, 0.0, 0.0, 1.0)\r
+FLT_OPT( targetfract, 0.0, 0.0, 1.0)\r
+FLT_OPT( queryfract, 0.0, 0.0, 1.0)\r
+FLT_OPT( fspenalty, 16.0, 0.0, FLT_MAX)\r
+FLT_OPT( sspenalty, 20.0, 0.0, FLT_MAX)\r
+FLT_OPT( seedt1, 13.0, 0.0, FLT_MAX)\r
+FLT_OPT( seedt2, 11.0, 0.0, FLT_MAX)\r
+FLT_OPT( lopen, 11.0, 0.0, FLT_MAX)\r
+FLT_OPT( lext, 1.0, 0.0, FLT_MAX)\r
+FLT_OPT( minh, 0.3, 0.0, FLT_MAX)\r
+FLT_OPT( xn, 8.0, 0.0, FLT_MAX)\r
+FLT_OPT( dn, 1.4, 0.0, FLT_MAX)\r
+FLT_OPT( xa, 1.0, 0.0, FLT_MAX)\r
+FLT_OPT( mindiv, 0.5, 0.0, 100.0)\r
+FLT_OPT( abskew, 2, 0.0, 100.0)\r
+FLT_OPT( abx, 8.0, 0.0, 100.0)\r
+FLT_OPT( minspanratio1, 0.7, 0.0, 1.0)\r
+FLT_OPT( minspanratio2, 0.7, 0.0, 1.0)\r
+\r
+FLAG_OPT( usersort)\r
+FLAG_OPT( exact)\r
+FLAG_OPT( optimal)\r
+FLAG_OPT( self)\r
+FLAG_OPT( ungapped)\r
+FLAG_OPT( global)\r
+FLAG_OPT( local)\r
+FLAG_OPT( xlat)\r
+FLAG_OPT( realign)\r
+FLAG_OPT( hash)\r
+FLAG_OPT( derep)\r
projects / mothur.git / blobdiff