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zkamvar/gvcf2csv.sh

Created September 8, 2017 20:43
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create csv from gvcf
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gvcf2csv.sh
#!/usr/bin/env bash
# This ridiculous script will take in a file as input and spit out comma-separated text for easier parsing.
# Usage:
# $ gvcf2csv.sh GVCF.err | column -t -s,
grep ProgressMeter $1 | \
awk -F" - " '{print $2}' | \
tail -n +2 | \
sed -E 's/[ ]\|[ ]/,/g' | \
sed -E "s/([0-9hmsw%])[ ]{3,}([0-9])/\1,\2/g"
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