1. FastqCleaner
  2. NAMESPACE
Browse code

fix ocurrencefilter

leandroroser authored on 15/04/2022 16:33:07
Showing 1 changed files
NAMESPACE
History View file @ 5dc3c3f
... ... 
@@ -41,6 +41,7 @@ importFrom(ShortRead,id)
41 41 
 importFrom(ShortRead,nFilter)
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 importFrom(ShortRead,sread)
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 importFrom(ShortRead,yield)
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+importFrom(ShortRead,occurrenceFilter)
44 45 
 importFrom(graphics,hist)
45 46 
 importFrom(methods,as)
46 47 
 importFrom(methods,is)
Browse code

push upstrean

leandroroser authored on 13/04/2022 02:49:52
Showing 1 changed files
NAMESPACE
History View file @ b48cb38
... ... 
@@ -37,7 +37,6 @@ importFrom(IRanges,width)
37 37 
 importFrom(S4Vectors,isConstant)
38 38 
 importFrom(ShortRead,FastqSampler)
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 importFrom(ShortRead,ShortReadQ)
40 
-importFrom(ShortRead,occurrenceFilter)
41 40 
 importFrom(ShortRead,id)
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 importFrom(ShortRead,nFilter)
43 42 
 importFrom(ShortRead,sread)
Browse code

Update NAMESPACE

Leandro Roser authored on 01/01/2022 23:04:04 • GitHub committed on 01/01/2022 23:04:04
Showing 1 changed files
NAMESPACE
History View file @ 901aa80
... ... 
@@ -37,7 +37,7 @@ importFrom(IRanges,width)
37 37 
 importFrom(S4Vectors,isConstant)
38 38 
 importFrom(ShortRead,FastqSampler)
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 importFrom(ShortRead,ShortReadQ)
40 
-importFrom(ShortRead, occurrenceFilter)
40 
+importFrom(ShortRead,occurrenceFilter)
41 41 
 importFrom(ShortRead,id)
42 42 
 importFrom(ShortRead,nFilter)
43 43 
 importFrom(ShortRead,sread)
Browse code

Update NAMESPACE

fix ocurrenceFilter

Leandro Roser authored on 01/01/2022 23:03:44 • GitHub committed on 01/01/2022 23:03:44
Showing 1 changed files
NAMESPACE
History View file @ c07172c
... ... 
@@ -37,6 +37,7 @@ importFrom(IRanges,width)
37 37 
 importFrom(S4Vectors,isConstant)
38 38 
 importFrom(ShortRead,FastqSampler)
39 39 
 importFrom(ShortRead,ShortReadQ)
40 
+importFrom(ShortRead, occurrenceFilter)
40 41 
 importFrom(ShortRead,id)
41 42 
 importFrom(ShortRead,nFilter)
42 43 
 importFrom(ShortRead,sread)
Browse code

fix conflicts

Leandro Roser authored on 14/02/2020 20:44:36
Showing 1 changed files
NAMESPACE
History View file @ cd6ff17
... ... 
@@ -1,15 +1,5 @@
1 
-<<<<<<< HEAD
2 1 
 # Generated by roxygen2: do not edit by hand
3 2
4 
-=======
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-<<<<<<< HEAD
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-# Generated by roxygen2: do not edit by hand
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-
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-=======
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-
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-useDynLib(FastqCleaner)
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->>>>>>> upstream/master
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->>>>>>> upstream/master
13 3 
 export(adapter_filter)
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 export(check_encoding)
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 export(complex_filter)
... ... 
@@ -28,10 +18,6 @@ export(trim3q_filter)
28 18 
 export(unique_filter)
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 import(Rcpp)
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 import(htmltools)
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-<<<<<<< HEAD
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-=======
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-<<<<<<< HEAD
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->>>>>>> upstream/master
35 21 
 importFrom(Biostrings,BStringSet)
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 importFrom(Biostrings,DNAString)
37 23 
 importFrom(Biostrings,DNAStringSet)
... ... 
@@ -63,24 +49,3 @@ importFrom(shinyBS,bsModal)
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 importFrom(shinyBS,bsPopover)
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 importFrom(stats,quantile)
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 useDynLib(FastqCleaner)
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-<<<<<<< HEAD
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-=======
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-=======
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-import(shiny, except=c(dataTableOutput, renderDataTable))
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-importFrom(shinyBS, bsPopover, bsModal, bsAlert)
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-importFrom(DT, dataTableOutput)
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-importFrom(DT, renderDataTable)
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-importFrom(S4Vectors, isConstant)
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-importFrom(graphics, hist)
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-importFrom(methods, as, is)
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-importFrom(stats, quantile)
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-importFrom(ShortRead, FastqStreamer, yield, sread, id, ShortReadQ, writeFastq,
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-        countLines, nFilter, qa, tables, FastqSampler, occurrenceFilter,
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-        narrow)
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-importFrom(Biostrings, BStringSet, PhredQuality, DNAString, width, start, end,
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-        dinucleotideFrequency, which.isMatchingStartingAt, as.matrix,
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-        oligonucleotideFrequency, reverse, replaceLetterAt, trimLRPatterns,
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-        reverseComplement,isMatchingStartingAt, isMatchingEndingAt, quality,
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-        DNAStringSet, subseq)
85 
->>>>>>> upstream/master
86 
->>>>>>> upstream/master
Browse code

fix conflicts

Leandro Roser authored on 14/02/2020 20:02:53
Showing 0 changed files
Browse code

test

Leandro Roser authored on 13/01/2020 00:55:12
Showing 1 changed files
NAMESPACE
History View file @ 0f1d081
... ... 
@@ -1,5 +1,5 @@
1 
+# Generated by roxygen2: do not edit by hand
1 2
2 
-useDynLib(FastqCleaner)
3 3 
 export(adapter_filter)
4 4 
 export(check_encoding)
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 export(complex_filter)
... ... 
@@ -18,19 +18,34 @@ export(trim3q_filter)
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 export(unique_filter)
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 import(Rcpp)
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 import(htmltools)
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-import(shiny, except=c(dataTableOutput, renderDataTable))
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-importFrom(shinyBS, bsPopover, bsModal, bsAlert)
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-importFrom(DT, dataTableOutput)
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-importFrom(DT, renderDataTable)
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-importFrom(S4Vectors, isConstant)
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-importFrom(graphics, hist)
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-importFrom(methods, as, is)
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-importFrom(stats, quantile)
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-importFrom(ShortRead, FastqStreamer, yield, sread, id, ShortReadQ, writeFastq,
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-        countLines, nFilter, qa, tables, FastqSampler, occurrenceFilter,
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-        narrow)
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-importFrom(Biostrings, BStringSet, PhredQuality, DNAString, width, start, end,
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-        dinucleotideFrequency, which.isMatchingStartingAt, as.matrix,
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-        oligonucleotideFrequency, reverse, replaceLetterAt, trimLRPatterns,
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-        reverseComplement,isMatchingStartingAt, isMatchingEndingAt, quality,
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-        DNAStringSet, subseq)
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+importFrom(Biostrings,BStringSet)
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+importFrom(Biostrings,DNAString)
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+importFrom(Biostrings,DNAStringSet)
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+importFrom(Biostrings,PhredQuality)
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+importFrom(Biostrings,dinucleotideFrequency)
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+importFrom(Biostrings,oligonucleotideFrequency)
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+importFrom(Biostrings,quality)
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+importFrom(Biostrings,replaceLetterAt)
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+importFrom(Biostrings,reverseComplement)
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+importFrom(Biostrings,trimLRPatterns)
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+importFrom(DT,dataTableOutput)
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+importFrom(DT,renderDataTable)
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+importFrom(IRanges,end)
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+importFrom(IRanges,narrow)
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+importFrom(IRanges,start)
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+importFrom(IRanges,width)
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+importFrom(S4Vectors,isConstant)
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+importFrom(ShortRead,FastqSampler)
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+importFrom(ShortRead,ShortReadQ)
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+importFrom(ShortRead,id)
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+importFrom(ShortRead,nFilter)
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+importFrom(ShortRead,sread)
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+importFrom(ShortRead,yield)
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+importFrom(graphics,hist)
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+importFrom(methods,as)
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+importFrom(methods,is)
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+importFrom(shinyBS,bsAlert)
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+importFrom(shinyBS,bsModal)
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+importFrom(shinyBS,bsPopover)
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+importFrom(stats,quantile)
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+useDynLib(FastqCleaner)
Browse code

new changes

Leandro Roser authored on 13/01/2020 00:20:39
Showing 0 changed files
Browse code

Initial commit

Leandro Roser authored on 06/05/2019 21:22:07
Showing 1 changed files
NAMESPACE
History View file @ ae4bfb1
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,51 @@
1 
+# Generated by roxygen2: do not edit by hand
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+
3 
+export(adapter_filter)
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+export(check_encoding)
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+export(complex_filter)
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+export(fixed_filter)
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+export(inject_letter_random)
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+export(launch_fqc)
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+export(length_filter)
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+export(n_filter)
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+export(qmean_filter)
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+export(random_length)
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+export(random_qual)
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+export(random_seq)
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+export(seq_filter)
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+export(seq_names)
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+export(trim3q_filter)
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+export(unique_filter)
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+import(Rcpp)
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+import(htmltools)
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+importFrom(Biostrings,BStringSet)
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+importFrom(Biostrings,DNAString)
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+importFrom(Biostrings,DNAStringSet)
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+importFrom(Biostrings,PhredQuality)
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+importFrom(Biostrings,dinucleotideFrequency)
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+importFrom(Biostrings,oligonucleotideFrequency)
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+importFrom(Biostrings,quality)
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+importFrom(Biostrings,replaceLetterAt)
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+importFrom(Biostrings,reverseComplement)
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+importFrom(Biostrings,trimLRPatterns)
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+importFrom(DT,dataTableOutput)
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+importFrom(DT,renderDataTable)
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+importFrom(IRanges,end)
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+importFrom(IRanges,narrow)
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+importFrom(IRanges,start)
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+importFrom(IRanges,width)
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+importFrom(S4Vectors,isConstant)
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+importFrom(ShortRead,FastqSampler)
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+importFrom(ShortRead,ShortReadQ)
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+importFrom(ShortRead,id)
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+importFrom(ShortRead,nFilter)
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+importFrom(ShortRead,sread)
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+importFrom(ShortRead,yield)
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+importFrom(graphics,hist)
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+importFrom(methods,as)
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+importFrom(methods,is)
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+importFrom(shinyBS,bsAlert)
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+importFrom(shinyBS,bsModal)
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+importFrom(shinyBS,bsPopover)
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+importFrom(stats,quantile)
51 
+useDynLib(FastqCleaner)
Browse code

add methods::is in ns

Leandro Roser authored on 19/05/2018 04:51:24
Showing 1 changed files
NAMESPACE
History View file @ 8a9077c
... ... 
@@ -20,12 +20,12 @@ import(Rcpp)
20 20 
 import(htmltools)
21 21 
 import(shiny, except=c(dataTableOutput, renderDataTable))
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 importFrom(shinyBS, bsPopover, bsModal, bsAlert)
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-importFrom(DT,dataTableOutput)
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-importFrom(DT,renderDataTable)
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-importFrom(S4Vectors,isConstant)
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-importFrom(graphics,hist)
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-importFrom(methods,as)
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-importFrom(stats,quantile)
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+importFrom(DT, dataTableOutput)
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+importFrom(DT, renderDataTable)
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+importFrom(S4Vectors, isConstant)
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+importFrom(graphics, hist)
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+importFrom(methods, as, is)
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+importFrom(stats, quantile)
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 importFrom(ShortRead, FastqStreamer, yield, sread, id, ShortReadQ, writeFastq,
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         countLines, nFilter, qa, tables, FastqSampler, occurrenceFilter,
31 31 
         narrow)
Browse code

corrections in documentation

Leandro Roser authored on 23/04/2018 06:02:35
Showing 1 changed files
NAMESPACE
History View file @ 5f08df1
... ... 
@@ -3,8 +3,6 @@ useDynLib(FastqCleaner)
3 3 
 export(adapter_filter)
4 4 
 export(check_encoding)
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 export(complex_filter)
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-export(cutLseq)
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-export(cutRseq)
8 6 
 export(fixed_filter)
9 7 
 export(inject_letter_random)
10 8 
 export(launch_fqc)
Browse code

fix warning

Leandro Roser authored on 19/04/2018 23:50:03
Showing 1 changed files
NAMESPACE
History View file @ 82c3903
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,38 @@
1 
+
2 
+useDynLib(FastqCleaner)
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+export(adapter_filter)
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+export(check_encoding)
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+export(complex_filter)
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+export(cutLseq)
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+export(cutRseq)
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+export(fixed_filter)
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+export(inject_letter_random)
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+export(launch_fqc)
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+export(length_filter)
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+export(n_filter)
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+export(qmean_filter)
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+export(random_length)
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+export(random_qual)
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+export(random_seq)
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+export(seq_filter)
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+export(seq_names)
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+export(trim3q_filter)
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+export(unique_filter)
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+import(Rcpp)
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+import(htmltools)
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+import(shiny, except=c(dataTableOutput, renderDataTable))
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+importFrom(shinyBS, bsPopover, bsModal, bsAlert)
25 
+importFrom(DT,dataTableOutput)
26 
+importFrom(DT,renderDataTable)
27 
+importFrom(S4Vectors,isConstant)
28 
+importFrom(graphics,hist)
29 
+importFrom(methods,as)
30 
+importFrom(stats,quantile)
31 
+importFrom(ShortRead, FastqStreamer, yield, sread, id, ShortReadQ, writeFastq,
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+        countLines, nFilter, qa, tables, FastqSampler, occurrenceFilter,
33 
+        narrow)
34 
+importFrom(Biostrings, BStringSet, PhredQuality, DNAString, width, start, end,
35 
+        dinucleotideFrequency, which.isMatchingStartingAt, as.matrix,
36 
+        oligonucleotideFrequency, reverse, replaceLetterAt, trimLRPatterns,
37 
+        reverseComplement,isMatchingStartingAt, isMatchingEndingAt, quality,
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+        DNAStringSet, subseq)