#!/bin/bash

CUR_DIR=`pwd`

if [ "$AUTOPKGTEST_TMP" = "" ]; then
	AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXX`

	trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM

fi

mkdir -p "$AUTOPKGTEST_TMP"/tests

# Copy configuration file
cp -a "${CUR_DIR}"/utils/nominal.ini "$AUTOPKGTEST_TMP"/tests

cd "$AUTOPKGTEST_TMP"/tests/


# Download Data
wget http://gembox.cbcb.umd.edu/mhap/raw/ecoli_p4_filtered.fastq.gz

# Extract Data
gunzip ecoli_p4_filtered.fastq.gz

seqtk seq -a ecoli_p4_filtered.fastq > reads.fasta
hinge correct-head reads.fasta reads.pb.fasta map.txt

fasta2DB ecoli reads.fasta
DBsplit -x500 -s100 ecoli     
HPC.daligner -t5 ecoli | bash -v

LAmerge ecoli.las ecoli.[1-5].las

rm ecoli.*.las 
DAScover -v -H10000 -mrepeat_mask ecoli.db ecoli.las
DASqv -c100 ecoli ecoli.las

# Run filter

mkdir log
hinge filter --db ecoli --las ecoli.las -x ecoli --config nominal.ini

# Get maximal reads

hinge maximal --db ecoli --las ecoli.las -x ecoli --config nominal.ini

# Run layout

hinge layout --db ecoli --las ecoli.las -x ecoli --config nominal.ini -o ecoli


# Run postprocessing ( networkx version needs to be downgraded to 1.x )

hinge clip ecoli.edges.hinges ecoli.hinge.list demo