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:
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
. Note -print_metrics
is deprecated in ADAM version
0.31.0 and will be removed in version 0.32.0.
flagstat¶
Runs the ADAM equivalent to the
SAMTools flagstat
command. Takes one required argument:
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 toSILENT.
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
. Note -print_metrics
is deprecated in ADAM version
0.31.0 and will be removed in version 0.32.0.
view¶
Runs the ADAM equivalent to the
SAMTools view
command.
Takes one required argument:
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
.