fq_count_timing.sh

#!/bin/bash -
set -o nounset                              # Treat unset variables as an error

TSV="count_timing.tsv"
CORES=2
TAGS=$1

echo -n "" > test.fq
for c in `seq 1 32`; do cat ../tests/pcs109_5k.fq >> test.fq; done
echo -e "Group\tBuffSize\tTime" > $TSV
for tag in $TAGS;
do
echo $tag
git checkout counting-$tag && go get ./... && go build
        for i in `seq 4 4 68` `seq 74 18 128` `seq 160 32 256` 1024 2048;
                do
                        for j in `seq 1 20`;
                        do
                        echo $tag $i $j
                        echo -e -n "$tag\t$i\t" >> $TSV
                        (./seqkit -j $CORES count -B $i test.fq 2>&1 | grep -v "[INFO]") >> $TSV
                        done
                done
done