Preprocess/out not properly initialized for unmated fastq files

[skoren]

There are no libX.seq/libX.seq.mates files created when running the pipeline on unmated fastq files. The following code should be added to line 1163 (in release 0.2):
elif lib.format == "fastq" and not lib.mated:
run_process("ln -s %s/Preprocess/in/%s %s/Preprocess/out/lib%d.seq"%(rundir, lib.fq, fname, rundir, lib.id), "Preprocess")
run_process("touch %s/Preprocess/out/lib%d.seq.mates"%(rundir, lib.id), "Preprocess")

and line 1230 should be:
soapd = soapd.replace("LIB%dQ1REPLACE"%(lib.id),"%s/Preprocess/out/%s"%(rundir,lib.f1.fname))