Lines Matching defs:RazerSOptions
50 struct RazerSOptions struct
53 TSpec spec;
54 bool forward; // compute forward oriented read matches
55 bool reverse; // compute reverse oriented read matches
56 double errorRate; // Criteria 1 threshold
57 unsigned maxHits; // output at most maxHits many matches
58 unsigned distanceRange; // output only the best, second best, ..., distanceRange best matches
59 bool purgeAmbiguous; // true..remove reads with more than maxHits best matches, false..keep them
60 CharString output; // name of result file
61 int _debugLevel; // level of verbosity
62 bool printVersion; // print version number
63 bool hammingOnly; // no indels
64 int trimLength; // if >0, cut reads to #trimLength characters
67 unsigned outputFormat; // 0..Razer format
70 bool dumpAlignment; // compute and dump the match alignments in the result files
71 unsigned genomeNaming; // 0..use Fasta id
73 unsigned readNaming; // 0..use Fasta id
77 unsigned sortOrder; // 0..sort keys: 1. read number, 2. genome position
79 unsigned positionFormat; // 0..gap space
81 const char *runID; // runID needed for gff output
85 int threshold; // threshold
86 int tabooLength; // taboo length
87 int repeatLength; // repeat length threshold
88 double abundanceCut; // abundance threshold
91 int libraryLength; // offset between two mates
92 int libraryError; // offset tolerance
93 unsigned nextPairMatchId; // use this id for the next mate-pair
96 bool matchN; // false..N is always a mismatch, true..N matches with all
97 unsigned char compMask[5];
100 __int64 countFiltration; // matches returned by the filter
101 __int64 countVerification; // matches returned by the verifier
102 double timeLoadFiles; // time for loading input files
103 double timeMapReads; // time for mapping reads
104 double timeDumpResults; // time for dumping the results
107 bool maqMapping;
108 int maxMismatchQualSum;
109 int mutationRateQual;
110 int absMaxQualSumErrors;
111 unsigned artSeedLength;
112 bool noBelowIdentity;
138 RazerSOptions() in RazerSOptions() argument