#!/bin/bash

# Temporary integration - this can be deleted when bior_build_catalog supports markdown creation and comparison stats.
# 1. Calls the reannotate toolkit to produce comparison statistics data
# 2. Feeds statistics data into bior_catalog_markdown to produce a markdown file with comparison stats

set -e
_bior_check_java_version
set +e

function usage
{
    echo "usage:  _bior_catalog_markdown_with_comparison_stats  <bior_overlap|bior_same_variant>  <old_catalog.tsv.bgz> <new_catalog.tsv.bgz>"
    exit 0;
}

if [ "$1" == "-h" ] || [ "$1" == "--help" ] ; then
    usage
fi

# input params
TOOLKIT_COMMAND=$1
OLD_CATALOG=$2
NEW_CATALOG=$3

TIME=`date +%s`

# dependencies
TMP_DIR=/local2/tmp/$USER/markdown$TIME
export REANNOTATE_HOME=/data5/bsi/bictools/src/reannotate/1.0.6
PATH=$REANNOTATE_HOME/bin:$PATH

mkdir $TMP_DIR

# create dummy bior_annotate.sh catalog_file
echo -e "OLD\t$TOOLKIT_COMMAND\t$OLD_CATALOG" > $TMP_DIR/catalog_file_old
echo -e "NEW\t$TOOLKIT_COMMAND\t$NEW_CATALOG" > $TMP_DIR/catalog_file_new

# create repo
REPO=$TMP_DIR/repo
mkdir $REPO
reannotate_create_release -r $REPO -v OLD -c $TMP_DIR/catalog_file_old
reannotate_create_release -r $REPO -v NEW -c $TMP_DIR/catalog_file_new

# create delta
reannotate_create_release_delta -r $REPO -o OLD -n NEW

# locate the comparison statistics data (delta_stats.json file)
DELTA_STATS_JSON=`find $REPO/pipeline_release_deltas/OLD___NEW | grep delta_stats.json`

# create markdown
bior_catalog_markdown -d $NEW_CATALOG -c $DELTA_STATS_JSON