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merenlab / illumina-utils

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.7+ pipeline).
GNU General Public License v2.0
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Suggested changes to iu-remove-ids-from-fastq #21

Closed ShaiberAlon closed 4 years ago

ShaiberAlon commented 4 years ago

I suggest (and plan to implement) the following changes to iu-remove-ids-from-fastq:

  1. Add a flag -G, --generate-output-for-survived-only
  2. -K, --keep-ids - if provided, then instead of removing the reads in the list, only the reads in the list will be kept (and the rest would be removed).