#!/bin/bash

## Trivial wrapper that just counts the number of lines in the input fastq


#Default settings
USE_THREADS=1



for i in "$@"; do
    case $i in
        --bascet-api)
        echo "bascet-mapcell-api 1.0" # Tell the API version this script conforms to
        exit 0
        ;;
        --expect-files)
        echo "*" # Tell which files should extracted from the input file. Can enable * to give them all. or "foo.txt,bar.txt"
        exit 0
        ;;
        --missing-file-mode)
        echo "skip" # Tell what to do if the expected files are not present
        exit 0
        ;;
        --compression-mode)
        echo "default" # Tell how to compress. options are default, uncompressed
        exit 0
        ;;
        --input-dir)
        INPUT_DIR="$2" # Directory with expected files from the cell
        shift # past argument=value
        shift
        ;;
        --output-dir)
        OUTPUT_DIR="$2"  # Where to store output to. this directory can be assumed to exist
        shift # past argument=value
        shift
        ;;
        --num-threads)
        USE_THREADS="$2" # How many threads to use
        shift # past argument=value
        shift
        ;;

        --preflight-check)
        #return 1 and echo sometine else here if something is wrong
        echo "MAPCELL-CHECK"
        exit 0
        ;;
        


        --default)
        DEFAULT=YES
        shift # past argument with no value
        ;;
        -*|--*)
        echo "Unknown option $i"  #not clear if we should keep?
        exit 1
        ;;
        *)
        ;;
    esac
done


######################## Execute script below #####################

if [ -z ${INPUT_DIR} ]; then 
echo "input directory is unset"; 
exit 1;
fi

if [ -z ${OUTPUT_DIR} ]; then 
echo "output directory is unset"; 
exit 1;
fi


echo "INPUT_DIR   = ${INPUT_DIR}"
echo "OUTPUT_DIR  = ${OUTPUT_DIR}"
echo "USE_THREADS  = ${USE_THREADS}"
#echo "Output:" $(wc -l "${INPUT_DIR}")

wc -l "${INPUT_DIR}/out.txt" > ${OUTPUT_DIR}/linecount


### The last line must be "MAPCELL-OK". 
echo "MAPCELL-OK"