From e6a7a10925315a1bcfa4508791efa5b3fbe2780f Mon Sep 17 00:00:00 2001 From: Vasco Elbrecht Date: Fri, 30 Jun 2017 00:23:27 +0200 Subject: [PATCH] bugfix change in comandd names in version 10 of usearch when PE merging --- JAMP/R/U_merge_PE.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/JAMP/R/U_merge_PE.R b/JAMP/R/U_merge_PE.R index b886d01..8d38ef5 100755 --- a/JAMP/R/U_merge_PE.R +++ b/JAMP/R/U_merge_PE.R @@ -1,7 +1,7 @@ # U_merge_PE v0.1 # maybe add option to split and merge large files automatically? -U_merge_PE <- function(files="latest", file1=NA, file2=NA, fastq_maxdiffs=99, fastq_maxdiffpct=99, fastq=T){ +U_merge_PE <- function(files="latest", file1=NA, file2=NA, fastq_maxdiffs=99, fastq_pctid=90, fastq=T){ Core(module="U_merge_PE") cat(file="../log.txt", c("\n","Version v0.1", "\n"), append=T, sep="\n") @@ -43,7 +43,7 @@ dir.create("_stats/merge_stats") log_names <- sub("_data", "_stats/merge_stats", new_names) log_names <- sub("_PE.fast[aq]", "_PE_log.txt", log_names) -cmd <- paste(" -fastq_mergepairs \"", file1, "\" -reverse \"", file2, "\" ", if(fastq){"-fastqout"} else {"-fastaout"}, " \"", new_names, "\"", " -report ", log_names, " -fastq_maxdiffs ", fastq_maxdiffs , " -fastq_maxdiffpct ", fastq_maxdiffpct ," -fastq_trunctail 0", sep="") +cmd <- paste(" -fastq_mergepairs \"", file1, "\" -reverse \"", file2, "\" ", if(fastq){"-fastqout"} else {"-fastaout"}, " \"", new_names, "\"", " -report ", log_names, " -fastq_maxdiffs ", fastq_maxdiffs , " -fastq_pctid ", fastq_pctid ," -fastq_trunctail 0", sep="") tab_exp <- NULL for (i in 1:length(cmd)){