gautil Documentation

This command line utility provides a collection of file processing tools. These tools allow for tasks such as converting between different file types, and the preprocessing of files prior to analysis.

gautil help

Provides a top level overview of the commands available and their specific usage.

gautil coverage

Create the .vcf.gz.covtsf file, which is used to draw zoomed out coverage

gautil coverage  <source>

Arguments: 
   source    The source file name
   
Flags:
  --refFolder=<refrence_file> the folder with a reference sequence matching 
                              the source

gautil fieldindex

Index the input file based on a selected field

gautil fieldindex <source> 

Arguments: 
   source    The source file name
   
Flags:
  --index=<index>  integer value of field to be indexed
  --path=<path>   path of the index file to be created 
  

gautil index

Create the .vcf.gz and .vcf.gz.tbi version of the input file that is genomically indexed

gautil index <source>

Arguments: 
   source    The source file name

Flags:
  --refFolder=<refrence_file> the folder with a reference sequence matching
                              the source

gautil precompute

Build an index/coverage for a BAM/IDF file

gautil precompute <source>
 
Arguments: 
   source    The source file name

gautil s3url

Generate an Amazon s3url based on input parameters

gautil s3url <S3Bucket> <S3Key> <S3AccessKey> <S3SecretKey> <ExpiresInNSeconds>

  Arguments:
  S3Bucket           Container of addressed objects
  S3Key              Object identifier in the bucket
  S3AccessKey        Amazon account identification
  S3SecretKey        Amazon account password
  ExpiresInNSeconds  The number of seconds the link will be live

gautil schema

Ouput the schema in json for the source (if it’s a directory, it will output a list of schema’s)

gautil schema <source> 
 
 Arguments: 
   source    The source file name

gautil writefasta

Output the file into the .fasta format

gautil writefasta <source> <destination> 
 
 Arguments: 
   source         The source file
   destination    The destination file

gautil writewig

Output the file into .wig format

gautil writewig <source> <destination> 
 
Arguments: 
   source         The source file name
   destination    The destination file name

gautil writetsf

Output the input file to the .tsf file format

gautil writetsf <source> <destination> --query=<subset_query>
 
Arguments: 
   source         The source file name
   destination    The destination file name

Optional Argument:
   query          Optional query such as chr1:851549-891052 that subsets
                  source to the query string. Requires that destination
                  is set. This is useful in creating subsets of files for
                  testing mostly.

gautil writevcf

Output the file into .vcf format

gautil writevcf <source> <destination> <options>
 
Arguments: 
   source         The source file name
   destination    The destination file name

Options:

   --fields=<idxs>   0-based indexes of fields to include in export (default all)

gautil lock

Lock and unlock a file, multiple files may be locked using an asterisk ‘*’. If a flag is not included in the command it will default to the lock command.

gautil lock --flag <source>

Arguments: 
  source    The source file name, the file name may be replaced
            with '*' to operate on all of the files in the directory 
            with the given file extension.

Flags:
  --set     Lock the files for editing
  --unset   Unlock the files for editing

gautil leftalign

Left align the features based on the included reference sequence.

gautil leftalign <source> <destination> 
 
Arguments: 
   source         The source file name
   destination    The destination file name
   
Flags:
  --refFolder=<refrence_file> the folder with a reference sequence matching 
                              the source