get-coverage-all-ways

#!/bin/bash
set -o errexit
set -o nounset
set -o pipefail
HAL=$1
for genome in $(halStats --genomes "$HAL"); do
    children=$(halStats --children "$genome" $HAL)
    if [ -n "$children" ]; then
        # Not a leaf genome
        echo "skipping $genome"
    else
        halCoverage "$HAL" $genome > "${HAL}.coverage.${genome}" &
        halCoverage "$HAL" $genome --collapse > "${HAL}.coverage.${genome}.collapsed" &
    fi
done
wait