Currently running mGEMS extract always names the files with the suffix "_1.fastq.gz", "_2.fastq.gz", "_3.fastq.gz" etc. depending on the number and order of the input files. It would be useful to add an option to change the name (or print to cout) to enable usage with calls like the following:
This may be faster than extracting both reads with a single command as compressing the reads sometimes takes more time than actually writing them. Current implementation does not allow the above call to work, because both calls will attempt to write to "input_1.fastq.gz".
Currently running
mGEMS extractalways names the files with the suffix "_1.fastq.gz", "_2.fastq.gz", "_3.fastq.gz" etc. depending on the number and order of the input files. It would be useful to add an option to change the name (or print to cout) to enable usage with calls like the following:This may be faster than extracting both reads with a single command as compressing the reads sometimes takes more time than actually writing them. Current implementation does not allow the above call to work, because both calls will attempt to write to "input_1.fastq.gz".