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