#!/bin/bash
set -e

pkg=stringtie
CUR_DIR=`pwd`

if [ "${AUTOPKGTEST_TMP}" = "" ] ; then
  AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
  trap "rm -rf ${AUTOPKGTEST_TMP}" 0 INT QUIT ABRT PIPE TERM
fi

cp ${CUR_DIR}/debian-tests-data/* -a "${AUTOPKGTEST_TMP}"

cd "${AUTOPKGTEST_TMP}"
gunzip -r *


MakeDb.py imgt -i S43_atleast-2.txz -s S43_atleast-2.fasta
echo "fca65a99ea3569b99196c50c42269946  S43_atleast-2_db-pass.tsv" >> checksums

CreateGermlines.py -d S43_atleast-2_db-pass.tsv -g dmask -r IMGT_Human_IGHV.fasta IMGT_Human_IGHD.fasta IMGT_Human_IGHJ.fasta
echo "8b76920fd30d640d34af22009621cc2e  S43_atleast-2_db-pass_germ-pass.tsv" >> checksums

ParseDb.py select -d S43_atleast-2_db-pass.tsv -f productive -u T
echo "7cf6dffe3d45414021d214da9ad6dc1e  S43_atleast-2_db-pass_parse-select.tsv" >> checksums

md5sum --check checksums

#Generates a randomised grouping

DefineClones.py -d S43_atleast-2_db-pass.tsv --act set --model ham --norm len --dist 0.16

BuildTrees.py -d S43_atleast-2_db-pass_clone-pass.tsv --outname ex --log ex.log --collapse --sample 3000 --clean all --nproc 1


