b5db9c06677afc3bd3a237ff3e3c171149d08725 donnak Wed Oct 23 12:58:50 2013 -0700 Incorporated code review feedback. #11972 diff --git src/blat/blat.c src/blat/blat.c index 9b49948..dbb5a51 100644 --- src/blat/blat.c +++ src/blat/blat.c @@ -85,56 +85,56 @@ " -q=type Query type. Type is one of:\n" " dna - DNA sequence\n" " rna - RNA sequence\n" " prot - protein sequence\n" " dnax - DNA sequence translated in six frames to protein\n" " rnax - DNA sequence translated in three frames to protein\n" " The default is dna.\n" " -prot Synonymous with -t=prot -q=prot.\n" " -ooc=N.ooc Use overused tile file N.ooc. N should correspond to \n" " the tileSize.\n" " -tileSize=N Sets the size of match that triggers an alignment. \n" " Usually between 8 and 12.\n" " Default is 11 for DNA and 5 for protein.\n" " -stepSize=N Spacing between tiles. Default is tileSize.\n" " -oneOff=N If set to 1, this allows one mismatch in tile and still\n" - " triggers an alignments. Default is 0.\n" + " triggers an alignment. Default is 0.\n" " -minMatch=N Sets the number of tile matches. Usually set from 2 to 4.\n" " Default is 2 for nucleotide, 1 for protein.\n" " -minScore=N Sets minimum score. This is the matches minus the \n" " mismatches minus some sort of gap penalty. Default is 30.\n" " -minIdentity=N Sets minimum sequence identity (in percent). Default is\n" " 90 for nucleotide searches, 25 for protein or translated\n" " protein searches.\n" " -maxGap=N Sets the size of maximum gap between tiles in a clump. Usually\n" " set from 0 to 3. Default is 2. Only relevent for minMatch > 1.\n" " -noHead Suppresses .psl header (so it's just a tab-separated file).\n" " -makeOoc=N.ooc Make overused tile file. Target needs to be complete genome.\n" " -repMatch=N Sets the number of repetitions of a tile allowed before\n" " it is marked as overused. Typically this is 256 for tileSize\n" " 12, 1024 for tile size 11, 4096 for tile size 10.\n" " Default is 1024. Typically comes into play only with makeOoc.\n" " Also affected by stepSize: when stepSize is halved, repMatch is\n" " doubled to compensate.\n" " -mask=type Mask out repeats. Alignments won't be started in masked region\n" " but may extend through it in nucleotide searches. Masked areas\n" " are ignored entirely in protein or translated searches. Types are:\n" " lower - mask out lower-cased sequence\n" " upper - mask out upper-cased sequence\n" " out - mask according to database.out RepeatMasker .out file\n" " file.out - mask database according to RepeatMasker file.out\n" - " -qMask=type Mask out repeats in query sequence. Similar to -mask above but\n" + " -qMask=type Mask out repeats in query sequence. Similar to -mask above, but\n" " for query rather than target sequence.\n" " -repeats=type Type is same as mask types above. Repeat bases will not be\n" " masked in any way, but matches in repeat areas will be reported\n" " separately from matches in other areas in the psl output.\n" " -minRepDivergence=NN Minimum percent divergence of repeats to allow \n" " them to be unmasked. Default is 15. Only relevant for \n" " masking using RepeatMasker .out files.\n" " -dots=N Output dot every N sequences to show program's progress.\n" " -trimT Trim leading poly-T.\n" " -noTrimA Don't trim trailing poly-A.\n" " -trimHardA Remove poly-A tail from qSize as well as alignments in \n" " psl output.\n" " -fastMap Run for fast DNA/DNA remapping - not allowing introns, \n" " requiring high %%ID. Query sizes must not exceed %d.\n" " -out=type Controls output file format. Type is one of:\n"