search

nh13 / DWGSIM

Whole Genome Simulator for Next-Generation Sequencing
GNU General Public License v2.0
92 stars 36 forks source link

Feature to disable the creation of each output file #39

Closed niemasd closed 7 years ago

niemasd commented 7 years ago

I am trying to use DWGSIM to simulate multiple replicates of WGS Illumina reads at 30x coverage on hg19, which creates massively large files. However, for my purposes, I don't care about the .bfast.fastq files (I only care about .bwa.read1.fastq and .bwa.read2.fastq), but because DWGSIM creates all of the files, I end up wasting space and cannot run as many in parallel because I need to wait for the running ones to finish, then delete everything I don't need and gzip .bwa.read1.fastq and .bwa.read2.fastq, then kick off more.

It would be a nice feature to be able to disable creating each of the output files so that I would be able to disable everything except for the .bwa.read1.fastq and .bwa.read2.fastq files that I want, which would more than halve the space taken by the output

nh13 commented 7 years ago

Sounds like a useful feature. Unfortunately I don't have a timetable for when I would look at implementing it (this is all Pro Bono), but I will keep it here in case I have spare time. I always welcome pull requests.

nh13 commented 7 years ago

@niemasd easier than I thought!

niemasd commented 7 years ago

Excellent, thanks so much for the quick implementation!