I added two new optional output files:
1) Masked: output file(s) for trimmed reads, with trimmed bases converted to lower case
2) Excluded: output file(s) for reads excluded by filters
I also added an option to replace trimmed bases with N’s, for programs that require all reads to be of the same length.
Finally, I added a new tag (TAG_LONG), and I made sure that all excluded reads have the correct tag assigned. I output the tag to the excluded file(s).
I added two new optional output files: 1) Masked: output file(s) for trimmed reads, with trimmed bases converted to lower case 2) Excluded: output file(s) for reads excluded by filters
I also added an option to replace trimmed bases with N’s, for programs that require all reads to be of the same length.
Finally, I added a new tag (TAG_LONG), and I made sure that all excluded reads have the correct tag assigned. I output the tag to the excluded file(s).