# Distributed by Chr (sh)

[View full source code on GitHub](https://github.com/dnanexus/dnanexus-example-applets/tree/master/Tutorials/bash/samtools_count_distr_chr_slice_sh)

## How is the SAMtools dependency provided?

The SAMtools dependency is resolved by declaring an Apt-Get package in the `dxapp.json` file's `runSpec.execDepends`.

```json
{
...
    "runSpec": {
   ...
      "execDepends": [
        {"name": "samtools"}
      ]
    }
...
}
```

For additional information, see `execDepends`

## Entry Points

Distributed bash-interpreter apps use bash functions to declare entry points. This app has the following entry points specified as bash functions:

* `main`
* `count_func`
* `sum_reads`

Entry points are executed on a new worker with its own system requirements. The instance type can be set in the `dxapp.json` file's `runSpec.systemRequirements`:

```json
{
  "runSpec": {
    ...
    "systemRequirements": {
      "main": {
        "instanceType": "mem1_ssd1_x4"
      },
      "count_func": {
        "instanceType": "mem1_ssd1_x2"
      },
      "sum_reads": {
        "instanceType": "mem1_ssd1_x4"
      }
    },
    ...
  }
}
```

### `main`

The `main` function slices the initial `*.bam` file and generates an index `*.bai` if needed. The input `*.bam` is the sliced into smaller `*.bam` files containing only reads from canonical chromosomes. First, the main function downloads the BAM file and gets the headers.

```shell
dx download "${mappings_sorted_bam}"
chromosomes=$( \
  samtools view -H "${mappings_sorted_bam_name}" \
  | grep "\@SQ" \
  | awk -F '\t' '{print $2}' \
  | awk -F ':' '{if ($2 ~ /^chr[0-9XYM]+$|^[0-9XYM]/) {print $2}}')
```

Sliced `*.bam` files are uploaded and their file IDs are passed to the `count_func` entry point using the [`dx-jobutil-new-job`](https://documentation.dnanexus.com/user/helpstrings-of-sdk-command-line-utilities) command.

```shell
if [ -z "${mappings_sorted_bai}" ]; then
  samtools index "${mappings_sorted_bam_name}"
else
  dx download "${mappings_sorted_bai}" -o "${mappings_sorted_bam_name}".bai
fi

count_jobs=()
for chr in $chromosomes; do
  seg_name="${mappings_sorted_bam_prefix}_${chr}".bam
  samtools view -b "${mappings_sorted_bam_name}" "${chr}" > "${seg_name}"
  bam_seg_file=$(dx upload "${seg_name}" --brief)
  count_jobs+=($(dx-jobutil-new-job -isegmentedbam_file="${bam_seg_file}" -ichr="${chr}" count_func))
done
```

Outputs from the `count_func` entry points are referenced as Job Based Object References (JBOR) and used as inputs for the `sum_reads` entry point.

```shell
for job in "${count_jobs[@]}"; do
  readfiles+=("-ireadfiles=${job}:counts_txt")
done

sum_reads_job=$(dx-jobutil-new-job "${readfiles[@]}" -ifilename="${mappings_sorted_bam_prefix}" sum_reads)
```

The output of the `sum_reads` entry point is used as the output of the main entry point via JBOR reference using the command `dx-jobutil-add-output`.

### `count_func`

This entry point downloads and runs the command `samtools view -c` on the sliced `*.bam`. The generated `counts_txt` output file is uploaded as the entry point's job output via the command `dx-jobutil-add-output`.

```shell
count_func ()
{
    echo "Value of segmentedbam_file: '${segmentedbam_file}'";
    echo "Chromosome being counted '${chr}'";
    dx download "${segmentedbam_file}";
    readcount=$(samtools view -c "${segmentedbam_file_name}");
    printf "${chr}:\t%s\n" "${readcount}" > "${segmentedbam_file_prefix}.txt";
    readcount_file=$(dx upload "${segmentedbam_file_prefix}".txt --brief);
    dx-jobutil-add-output counts_txt "${readcount_file}" --class=file
}
```

### `sum_reads`

The `main` entry point triggers this sub job, providing the output of `count_func` as an input. This entry point gathers all the files generated by the `count_func` jobs and sums them.

This function returns `read_sum_file` as the entry point output.

```shell
sum_reads ()
{
    set -e -x -o pipefail;
    printf "Value of read file array %s" "${readfiles[@]}";
    echo "Filename: ${filename}";
    echo "Summing values in files and creating output read file";
    for read_f in "${readfiles[@]}";
    do
        echo "${read_f}";
        dx download "${read_f}" -o - >> chromosome_result.txt;
    done;
    count_file="${filename}_chromosome_count.txt";
    total=$(awk '{s+=$2} END {print s}' chromosome_result.txt);
    echo "Total reads: ${total}" >> "${count_file}";
    readfile_name=$(dx upload "${count_file}" --brief);
    dx-jobutil-add-output read_sum_file "${readfile_name}" --class=file
}
```