#!/bin/bash

#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 "contigs.fa" # 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
        ;;
              --recommend-threads)
              echo "1" # Tell how many threads that is recommended by default
              exit 0
              ;;
        --preflight-check)
        if ! command -v kmc 2>&1 >/dev/null
        then
          echo "kmc could not be found"
          exit 1
        fi
        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 "Building a KMC3 database from contigs"

echo "INPUT_DIR   = ${INPUT_DIR}"
echo "OUTPUT_DIR  = ${OUTPUT_DIR}"
echo "USE_THREADS  = ${USE_THREADS}"

#Can assume to be running in the output directory


KMC_TEMP=.
INPUT_FILE_NAME=${INPUT_DIR}/contigs.fa
#OUTPUT_DB=kmc.db
#OUTPUT_DUMP=kmc_dump.txt


#Need to provide list of input files, as a file
echo $INPUT_FILE_NAME >  inlist.txt

#Run KMC on FASTA input. Note that KMC cannot handle $vars as arguments for some reason!!
kmc -cs2000000000  -k31 -ci=1 -fa  @inlist.txt  kmc  .

#kmc [options] <input_file_name> <output_file_name> <working_directory>
#-f<a/q/m/bam/kmc> - input in FASTA format (-fa), FASTQ format (-fq), multi FASTA (-fm) or BAM (-fbam) or KMC(-fkmc); default: FASTQ
#-k<len>           - k-mer length (k from 1 to 256; default: 25)
#-cs<value>        - maximal value of a counter (default: 255)                               u32::MAX-1 = 4_294_967_294   has been used
#-ci<value>        - exclude k-mers occurring less than <value> times (default: 2)


### To enable reading from the database, dump as txt  (in the future, possible to read KMC database from zip directly)
#kmc_tools transform $OUTPUT_DB dump $OUTPUT_DUMP  cannot do $arg for some reason
kmc_tools transform kmc dump kmc_dump.txt

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