R/trimFront.R

In HIVDiversity/MotifBinner2: Processes NGS Primer ID Datasets

#library(Rcpp)
#library(ShortRead)
#
#seq_dat <- readFastq('test_dat.fastq')
##seq_dat <- readFastq('/fridge/data/MotifBinner2_test/raw/CAP256_3100_030wpi_v1v2_20k_R1.fastq')
#seq_dat <- readFastq('/fridge/data/MotifBinner2_test/raw/CAP256_3100_030wpi_v1v2_R1.fastq')
#
#prefix <- 'TATGGGAYSAAAGYCTMAARCCATGTG'
#
#print(seq_dat@sread)
#
#cat('\n\n\n\n\n\n\n\n\n'); sourceCpp('trimFront.cpp')
#trimmed <- trimFront_cpp(as.character(seq_dat@sread),
#                        as.character(seq_dat@quality@quality),
#                        prefix, c(13, 7, 7))
#
#str(trimmed)