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Destroyed ScriptManager (markdown)
Destroyed ScalingFactor (markdown)
Destroyed Read Analysis (markdown)
Destroyed Coordinate Manipulation (markdown)
Destroyed BAM Statistics (markdown)
Destroyed File Formats (markdown)
Destroyed BAM Manipulation (markdown)
Destroyed BAM Format Converter (markdown)
Updated Home (markdown)
Add initial toolgroup pages This is committing just a skeleton to see if this wiki directory structure works with the github interface or if I should strip out the directory organization of markdown pages and keep them all in a single file. Also checking if images saved in the wiki repo can be accessed by the markdown pages. Essentially there is a main wiki page, one for File-Format help, one as a general overview of the command line structure, and then a page for each tool group with a section for each tool.
link to Command Line Overview page
reformat new line spacing of note in table
Outline and initialize Command Line Overview with some extra info on some shared options
Outline Home Page to mimic Picard