[Bioc-devel] Append/combine option for filterFastq and similar?

Ryan C. Thompson rct at thompsonclan.org
Tue Apr 21 23:18:58 CEST 2015


Often when sequence data is delivered to me, I receive each sample in 
several input files. Generally I want to get them into a single file 
ASAP, and the filterFastq step would be a convenient place to do it. Is 
there any possibility to add some way to append to an output file, or 
maybe automatically combine the outputs of any files with the same 
destination file. For example:

filterFastq(files=c("input1.fastq", "input2.fastq"), 
destinations="output.fastq", ...)

could process both input files and write their combined output to the 
one specified output file. Normal recycling rules would apply for the 
"destinations" argument, and input files would be grouped by destination 
file and each processed sequentially into that destination file. (This 
design is kind of magic, but it avoids the annoying pattern of having to 
process files one-by-one in a loop with append=FALSE for the first file 
and append=TRUE for the rest. (Also appending to a compressed fastq 
might not work?)


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