> For the complete documentation index, see [llms.txt](https://documentation.dnanexus.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://documentation.dnanexus.com/getting-started/developer-tutorials/bash/samtools-count.md).

# SAMtools count

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

This applet performs a basic `samtools view -c {bam}` command, referred to as "SAMtools count", on the DNAnexus Platform.

## Download BAM Files

For bash scripts, inputs to a job execution become environment variables. The inputs from the `dxapp.json` file are formatted as shown in the following example:

```json
{
  "inputSpec": [
    {
      "name": "mappings_bam",
      "label": "Mapping",
      "class": "file",
      "patterns": ["*.bam"],
      "help": "BAM format file."
    }
  ]
}
```

The object `mappings_bam`, a DNAnexus link containing the file ID of that file, is available as an environment variable in the applet's execution. Use the command `dx download` to download the BAM file. By default, downloading a file preserves the filename of the object on the platform.

```shell
dx download "${mappings_bam}"
```

## SAMtools Count

Use the bash helper variable `mappings_bam_name` for file inputs. For these inputs, the DNAnexus Platform creates a bash variable `[VARIABLE]_name` that holds the platform filename. Because the file was downloaded with default parameters, the worker filename matches the platform filename. The helper variable `[VARIABLE]_prefix` contains the filename minus any suffixes specified in the input field patterns (for example, the platform removes the trailing `.bam` to create `[VARIABLE]_prefix`).

```shell
readcount=$(samtools view -c "${mappings_bam_name}")
echo "Total reads: ${readcount}" > "${mappings_bam_prefix}.txt"
```

## Upload Result

Use the [`dx upload`](/user/helpstrings-of-sdk-command-line-utilities.md#upload) command to upload data to the platform. This uploads the file into the job container, a temporary project that holds onto files associated with the job. When running the command `dx upload` with the flag `--brief`, the command returns only the file ID.

```shell
counts_txt_id=$(dx upload "${mappings_bam_prefix}.txt" --brief)
```

Job containers are an integral part of the execution process. To learn more see [Containers for Execution](/developer/api/running-analyses/containers-for-execution.md).

## Associate With Output

The output of an applet must be declared before the applet is even built. Looking back to the `dxapp.json` file, you see the following:

```json
{
  "name": "counts_txt",
  "class": "file",
  "label": "Read count file",
  "patterns": [
    "*.txt"
  ],
  "help": "Output file with Total reads as the first line."
}
```

The applet declares a **file** type output named `counts_txt`. In the applet script, specify which file is associated with the output `counts_txt`. On job completion, this file is copied from the temporary job container to the project that launched the job.

```shell
dx-jobutil-add-output counts_txt "${counts_txt_id}" --class=file
```


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