| /dports/biology/bbmap/bbmap/current/shared/ |
| H A D | TrimRead.java | 69 float trimq, float avgErrorRate, int minlen){ in trim() argument
96 float trimq, float avgErrorRate, int minResult){ in trimFast() argument
152 a=(trimLeft ? testLeft(bases, qual, (byte)trimq) : 0); in trimFast()
153 b=(trimRight ? testRight(bases, qual, (byte)trimq) : 0); in trimFast()
174 trimq=(byte)trimq_; in TrimRead()
376 if(qual==null){return trimq<0 ? 0 : testLeftN(bases);} in testLeft()
384 if(q>trimq){good++;} in testLeft()
399 final int thresh=Tools.max(window*trimq, 1); in testRightWindow()
417 if(qual==null){return trimq<0 ? 0 : testRightN(bases);} in testRight()
425 if(q>trimq){good++;} in testRight()
[all …]
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| /dports/devel/R-cran-remotes/remotes/R/ |
| H A D | json.R | 158 trimq(token)
164 trimq <- function(x) { function
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| /dports/biology/bbmap/bbmap/current/var2/ |
| H A D | Realign.java | 81 parser.trimq=trimq; in Realign()
152 trimq=parser.trimq; in Realign()
523 private float trimq=10;
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| /dports/biology/bbmap/bbmap/pytools/filter_param/ |
| H A D | rnawohuman.config | 1 rna=t minlength=49 qtrim=r maq=10 trimq=6 trimfragadapter=t phix=t maxns=1 mlf=0.33 removehuman=f r…
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| H A D | chip-seq.config | 1 rna=f trimfragadapter=t qtrim=r trimq=6 maxns=1 maq=10 minlen=49 phix=t khist=t removehuman=t remov…
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| H A D | clrs.config | 1 rna=f minlength=50 library=clrs phix=t qtrim=r trimq=6 maxns=1 maq=10 removehuman=t removedog=t rem…
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| H A D | lfpe.config | 1 rna=f minlength=31 library=lfpe phix=t qtrim=r trimq=6 maxns=1 maq=10 removehuman=t removedog=t rem…
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| H A D | smrna.config | 1 rna=t trimfragadapter=t qtrim=r trimq=6 maxns=1 maq=10 minlen=17 mlf=0 khist=t trimk=23 mink=3 hdis…
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| H A D | plant-2x150.config | 1 rna=f trimfragadapter=t qtrim=r trimq=6 maxns=1 maq=10 minlen=50 phix=t removehuman=t removedog=t r…
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| H A D | plant-2x250.config | 1 rna=f trimfragadapter=t qtrim=r trimq=6 maxns=1 maq=10 minlen=75 phix=t removehuman=t removedog=t r…
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| H A D | 3primerna.config | 1 rna=t trimfragadapter=t qtrim=r trimq=6 maxns=1 maq=10 minlen=25 mlf=0.33 phix=t removehuman=t remo…
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| H A D | dna.config | 1 rna=f trimfragadapter=t qtrim=r trimq=6 maxns=1 maq=10 minlen=49 mlf=0.33 phix=t removehuman=t remo…
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| H A D | metagenome.config | 1 rna=f trimfragadapter=t qtrim=r trimq=0 maxns=3 maq=3 minlen=51 mlf=0.33 phix=t removehuman=t remov…
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| H A D | fungal.config | 1 rna=f trimfragadapter=t qtrim=r trimq=0 maxns=0 maq=13 minlen=41 mlf=0.33 phix=t removehuman=t remo…
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| H A D | nextera-lmp.config | 1 rna=f nextera=t phix=t minlength=31 qtrim=r trimq=6 maxns=1 maq=10 trimfragadapter=t removehuman=t …
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| H A D | rna.config | 1 rna=t minlength=49 qtrim=r maq=10 trimq=6 trimfragadapter=t phix=t maxns=1 mlf=0.33 removehuman=t r…
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| H A D | clip-pe.config | 1 rna=f minlength=31 library=clip cliplinker=CATG phix=t qtrim=r trimq=6 maxns=1 maq=10 removehuman=t…
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| H A D | bisulphite.config | 1 rna=f trimfragadapter=t qtrim=r trimq=6 maxns=1 maq=10 minlen=49 mlf=0.33 phix=t removehuman=t remo…
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| H A D | itag.config | 1 rna=f trimfragadapter=t removehuman=f removedog=f removecat=f removemouse=f phix=t qtrim=f trimq=0 …
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| H A D | microtrans.config | 1 rna=t minlength=49 qtrim=r maq=10 trimq=6 trimfragadapter=t phix=t maxns=1 mlf=0.33 removehuman=t r…
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| H A D | viral-metagenome.config | 1 rna=f trimfragadapter=t qtrim=r trimq=0 maxns=3 maq=3 minlen=51 mlf=0.33 phix=t removehuman=t remov…
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| H A D | mtaa.config | 1 rna=t trimfragadapter=t qtrim=r trimq=0 maxns=1 maq=10 minlen=51 mlf=0.33 phix=t removeribo=t remov…
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| H A D | cell-enrichment.config | 1 rna=f minlength=51 phix=t trimfragadapter=t maxns=1 mlf=0.33 qtrim=r trimq=6 maq=10 minlen=49 khist…
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| /dports/biology/bbmap/bbmap/current/hiseq/ |
| H A D | AnalyzeFlowCell.java | 101 trimq=parser.trimq; in AnalyzeFlowCell()
128 parser.trimq=trimq; in parse()
744 if(trimq>0){ in processReadPair()
745 TrimRead.trimFast(r1, trimLeft, trimRight, trimq, trimE, 0); in processReadPair()
746 if(r2!=null){TrimRead.trimFast(r2, trimLeft, trimRight, trimq, trimE, 0);} in processReadPair()
1039 private float trimq=-1; field in AnalyzeFlowCell
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| /dports/biology/bbmap/bbmap/current/jgi/ |
| H A D | SplitPairsAndSingles.java | 61 parser.trimq=trimq; in SplitPairsAndSingles()
137 trimq=parser.trimq; in SplitPairsAndSingles()
624 int x=TrimRead.trimFast(r1, qtrimLeft, qtrimRight, trimq, trimE, 1); in processPair()
633 int x=TrimRead.trimFast(r2, qtrimLeft, qtrimRight, trimq, trimE, 1); in processPair()
783 private float trimq=6; field in SplitPairsAndSingles
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