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#####################
# Default option run:
#####################
../../run_discoSnp++.sh -r fof.txt -T -P 1
if [ $? -ne 0 ] ; then
echo "*** Default option FAILURE:"
echo "*** discoSnp failure"
exit 1
fi
mv discoRes_k_31_c_3_D_100_P_1_b_0_coherent.fa ref_discoRes_k_31_c_3_D_100_P_1_b_0_coherent.fa
mv discoRes_k_31_c_3_D_100_P_1_b_0_coherent.vcf ref_discoRes_k_31_c_3_D_100_P_1_b_0_coherent.vcf
######################################################
# With reference run (using previously created graph):
######################################################
../../run_discoSnp++.sh -r fof.txt -T -G humch1_first_5M.fasta -g discoRes_k_31_c_3.h5 -P 1
if [ $? -ne 0 ] ; then
echo "*** With mapping on ref FAILURE:"
echo "*** discoSnp failure"
exit 1
fi
mv discoRes_k_31_c_3_D_100_P_1_b_0_coherent.vcf ref_with_mapping_discoRes_k_31_c_3_D_100_P_1_b_0_coherent.vcf
mv discoRes_k_31_c_3_D_100_P_1_b_0_coherent_for_IGV.vcf ref_with_mapping_discoRes_k_31_c_3_D_100_P_1_b_0_coherent_for_IGV.vcf
#####################
# CLOSE SNPS option run:
#####################
../../run_discoSnp++.sh -r fof.txt -T -P 10
if [ $? -ne 0 ] ; then
echo "*** With close SNPS FAILURE:"
echo "*** discoSnp failure"
exit 1
fi
mv discoRes_k_31_c_3_D_100_P_10_b_0_coherent.fa ref_discoRes_k_31_c_3_D_100_P_10_b_0_coherent.fa
mv discoRes_k_31_c_3_D_100_P_10_b_0_coherent.vcf ref_discoRes_k_31_c_3_D_100_P_10_b_0_coherent.vcf
######################################################
# With reference run (using previously created graph):
######################################################
../../run_discoSnp++.sh -r fof.txt -T -G humch1_first_5M.fasta -g discoRes_k_31_c_3.h5 -P 10
if [ $? -ne 0 ] ; then
echo "*** With close SNPS and mapping on ref FAILURE:"
echo "*** discoSnp failure"
exit 1
fi
mv discoRes_k_31_c_3_D_100_P_10_b_0_coherent.vcf ref_with_mapping_discoRes_k_31_c_3_D_100_P_10_b_0_coherent.vcf
mv discoRes_k_31_c_3_D_100_P_10_b_0_coherent_for_IGV.vcf ref_with_mapping_discoRes_k_31_c_3_D_100_P_10_b_0_coherent_for_IGV.vcf
# create archive
zip -r data_test_disco.zip humch1_00096_reads.fasta.gz humch1_00100_reads.fasta.gz humch1_first_5M.fasta ref_discoRes_k_31_c_3_D_100_P_10_b_0_coherent.fa ref_discoRes_k_31_c_3_D_100_P_10_b_0_coherent.vcf ref_discoRes_k_31_c_3_D_100_P_1_b_0_coherent.fa ref_discoRes_k_31_c_3_D_100_P_1_b_0_coherent.vcf ref_with_mapping_discoRes_k_31_c_3_D_100_P_10_b_0_coherent.vcf ref_with_mapping_discoRes_k_31_c_3_D_100_P_10_b_0_coherent_for_IGV.vcf ref_with_mapping_discoRes_k_31_c_3_D_100_P_1_b_0_coherent.vcf ref_with_mapping_discoRes_k_31_c_3_D_100_P_1_b_0_coherent_for_IGV.vcf
#(update
#Mettre sur bioinformatique
#OLD: scp data_test_disco.zip ppeterlo@scm.gforge.inria.fr:/home/groups/gatb-discosnp/htdocs)
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