#!/bin/bash

#module load util/coreutils/8.27

JUICER_JAR=/data/projects/phillippy/software/juicer/cpuscripts/juicer_tools_0.7.0.jar
SALSA_OUT_DIR=$1
SCRIPT_PATH=$BASH_SOURCE
SCRIPT_PATH=`dirname $SCRIPT_PATH`

samtools faidx ${SALSA_OUT_DIR}/scaffolds_FINAL.fasta

cut -f 1,2 ${SALSA_OUT_DIR}/scaffolds_FINAL.fasta.fai > ${SALSA_OUT_DIR}/chromosome_sizes.tsv

python ${SCRIPT_PATH}/alignments2txt.py -b ${SALSA_OUT_DIR}/alignment_iteration_1.bed  -a ${SALSA_OUT_DIR}/scaffolds_FINAL.agp -l ${SALSA_OUT_DIR}/scaffold_length_iteration_1 > ${SALSA_OUT_DIR}/alignments.txt

awk '{if ($2 > $6) {print $1"\t"$6"\t"$7"\t"$8"\t"$5"\t"$2"\t"$3"\t"$4} else {print}}'  ${SALSA_OUT_DIR}/alignments.txt | sort -k2,2d -k6,6d -T $PWD --parallel=16 | awk 'NF'  > ${SALSA_OUT_DIR}/alignments_sorted.txt

java -jar ${JUICER_JAR} pre ${SALSA_OUT_DIR}/alignments_sorted.txt ${SALSA_OUT_DIR}/salsa_scaffolds.hic ${SALSA_OUT_DIR}/chromosome_sizes.tsv