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#!/bin/bash | |
# ******REQUIRES SAMTOOLS****** | |
#This is a sam assembly collapser using coordinates and strand as the "unique insert" identifiers, keeping the read with the highest mapping quality | |
#Written/assembled by Jake Enk and Alison Devault (and named by Nathalie Mouttham) June 3, 2013 | |
# Usage: $ aweSAM_collapser [input samfile] [output collapsed samfile] | |
# PROCESS: |