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#!/bin/bash
run_discoSnp++.sh -r fof.txt -T
diff discoRes_k_31_c_3_D_100_P_3_b_0_coherent.fa ref_discoRes_k_31_c_3_D_100_P_3_b_0_coherent.fa
if [ $? -ne 0 ] ; then
echo "*** Test: FAILURE on diff .fa"
exit 1
fi
# we do not want to compare fildate lines since they are de facto not similar
awk '!/##filedate=/' discoRes_k_31_c_3_D_100_P_3_b_0_coherent.vcf > discoRes_a.vcf
awk '!/##filedate=/' ref_discoRes_k_31_c_3_D_100_P_3_b_0_coherent.vcf > discoRes_b.vcf
diff discoRes_a.vcf discoRes_b.vcf
if [ $? -ne 0 ] ; then
echo "*** Test: FAILURE on diff .vcf"
exit 1
fi
rm -fr discoRes_* reference_genome.fa.*
echo "*** Test: OK"
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