# Printing tools¶

The printing tools provide some form of user readable view of an ADAM file. These commands are useful for both quality control and debugging.

## print¶

Dumps a Parquet file to either the console or a text file as JSON. Takes one required argument:

1. FILE(S): The file paths to load. These must be Parquet formatted files.

This command has several options:

• -pretty: Pretty prints the JSON output.
• -o: Provides a path to save the output dump to, instead of writing the output to the console.

This command does not support Parquet output, so the only default options that this command supports is -print_metrics.

## flagstat¶

Runs the ADAM equivalent to the SAMTools flagstat command. Takes one required argument:

1. INPUT: The input path. A file containing reads in any of the supported ADAM read input formats.

This command has several options:

• -stringency: Sets the validation stringency for various operations. Defaults to SILENT. See validation stringency for more details.
• -o: Provides a path to save the output dump to, instead of writing the output to the console.

This command does not support Parquet output, so the only default options that this command supports is -print_metrics.

## view¶

Runs the ADAM equivalent to the SAMTools view command. Takes one required argument:

1. INPUT: The input path. A file containing reads in any of the supported ADAM read input formats.

In addition to the default options, this command supports the following options:

• -o: Provides a path to save the output dump to, instead of writing the output to the console. Format is autodetected as any of the ADAM read outputs.
• -F/-f: Filters reads that either match all (-f) or none (-F) of the flag bits.
• -G/-g: Filters reads that either mismatch all (-g) or none (-G) of the flag bits.
• -c: Prints the number of reads that (mis)matched the filters, instead of the reads themselves. Conflicts with -o.