help_message.txt

-h:
 Prints this help message


Compression,
 general command:
./gpress (options) [inputfile] [folder]
The “inputfile" is compressed and stored in the specified “folder”.
For sparse expression files, "inputfile" are three files: [input matrix] [input genes] [input barcodes]


Options:
-cw: annotation file is compressed without random access. No parameters needed.
-c <block_size>: annotation file is compressed with specified block_size (2000 by default).
-e <block_size>: dense expression file is compressed with specified block_size (2000 by default).
-sparse <block_size>: sparse expression file is compressed with specified block_size (2000 by default).

Decompression/queries:
./gpress (options/parameters) [folder]
Will retrieve information from compressed files in “folder”.
Output from queries is printed to terminal by default. Add “> [outputfile]” to print to a file instead.


Options/Parameters:
-dc [filetype]: Decompresses annotation file without random access, <filetype> must be either gff3 or gtf.
-q -id [id]: Retrieve items with identifier “id” from the ANNOTATION file.
-q -id -f [id]: Retrieve item with identifier “id” and its parents/children from the ANNOTATION file.
-q -id: Allows for multiple ID searches on the ANNOTATION file, and also to retrieve parent/children items.
-q -range [start] [end] [chromosome]: Retrieve items from the ANNOTATION file that fall within the provided range.
-qe [id]: Retrieve items with identifier “id” from the ANNOTATION and DENSE EXPRESSION files.
-qer [start] [end] [chromosome]: Retrieve items from the ANNOTATION and DENSE EXPRESSION files that fall within the provided range.
-qs [id]: Retrieve items with identifier “id” from the ANNOTATION and SPARSE EXPRESSION files.
-qsr [start] [end] [chromosome]: Retrieve items from the ANNOTATION and SPARSE EXPRESSION files that fall within the provided range.