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jts / sga

de novo sequence assembler using string graphs
http://genome.cshlp.org/content/22/3/549
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send to stdout #94

Open macmanes opened 8 years ago

macmanes commented 8 years ago

Enhancement as per Twitter discussion: https://twitter.com/macmanes/status/655917967884980224

Allow corrected reads to be sent to the stdout. There might be several other places where this could save a lot of time. For example:

sga prepare | sga index | sga correct | bwa mem > out.sam
channsoden commented 8 years ago

I've been trying to get this to work as well. I've got the pipeline working for preprocess and index, but am stuck at piping both the bwt index and the preprocessed reads to correct. It seems like this should work:

ln -s /dev/stdout mystdout.bwt
ln -s /dev/sd/63 in63.bwt
ln -s /dev/sd/62 in62
sga correct -p in63 -o correctedreads.fastq -t 1 in62 <(sga index -a ropebwt -t 1 -p mystdout --no-sai --no-reverse filteredreads.fastq) <(cat filteredreads.fastq)

Except this throws an error from the option parser: correct: too many arguments

Could the option parser just be modified to accept this kind of process substitution?