aaiezza / flick Goto Github PK

Instead of putting the output file name at the end of the command, put it after an --output flag and allow for multiple input paths to be given for flicking at the end of the command

Currently, the FLiCK platform performs ZIP compression on files it has no built modules for. There could be integration of gzip and bzip2 and an adjusting flag for what type of compression to perform on these module-less files.

Regardless of the extension of the input file, force a module to work on it anyways

Flick doesn't like this! Seems to use the last registered module encountered.
There should be an error message when a repeat extension module attempts to be registered.

Zip4j crashes unflick when given a file that is not a zip file or, more appropriately, a flick file:

C:\git\FLiCK\test_resources>java -cp ..\build\libs\flick-0.4.1.jar edu.rit.flick.util.Unflick -v SRR390728_1.fq net.lingala.zip4j.exception.ZipException: zip headers not found. probably not a zip file at net.lingala.zip4j.core.HeaderReader.readEndOfCentralDirectoryRecord(HeaderReader.java:122) at net.lingala.zip4j.core.HeaderReader.readAllHeaders(HeaderReader.java:78) at net.lingala.zip4j.core.ZipFile.readZipInfo(ZipFile.java:425) at net.lingala.zip4j.core.ZipFile.extractAll(ZipFile.java:475) at net.lingala.zip4j.core.ZipFile.extractAll(ZipFile.java:451) at edu.rit.flick.DefaultFlickFile.inflate(DefaultFlickFile.java:238) at edu.rit.flick.FlickFile.inflate(FlickFile.java:36) at edu.rit.flick.util.Unflick.main(Unflick.java:57)

• There should a be a list flag to list all of the file extensions and modules that exist.
• Also another flag to show the option set for a given module.
• Maybe it is OK to have multiple modules for the same extensions (multiple modules issue), but be able to make one of them default and select which one you wish to use with some flag.